Method for Using Gene Expression to Determine Prognosis of Prostate Cancer

ABSTRACT

Molecular assays that involve measurement of expression levels of prognostic biomarkers, or co-expressed biomarkers, from a biological sample obtained from a prostate cancer patient, and analysis of the measured expression levels to provide information concerning the likely prognosis for said patient, and likelihood that said patient will have a recurrence of prostate cancer, or to classify the tumor by likelihood of clinical outcome or TMPRSS2 fusion status, are provided herein.

This application is a continuation of U.S. application Ser. No. 16/282,540, filed Feb. 22, 2019, which is a continuation of U.S. application Ser. No. 14/887,605, filed Oct. 20, 2015, now U.S. Pat. No. 10,260,104, issued Apr. 16, 2019, which is a continuation of U.S. application Ser. No. 13/190,391, filed Jul. 25, 2011, which claims the benefit of priority to U.S. Provisional Application Nos. 61/368,217, filed Jul. 27, 2010; 61/414,310, filed Nov. 16, 2010; and 61/485,536, filed May 12, 2011, all of which are hereby incorporated by reference.

TECHNICAL FIELD

The present disclosure relates to molecular diagnostic assays that provide information concerning methods to use gene expression profiles to determine prognostic information for cancer patients. Specifically, the present disclosure provides genes and microRNAs, the expression levels of which may be used to determine the likelihood that a prostate cancer patient will experience a local or distant cancer recurrence.

INTRODUCTION

Prostate cancer is the most common solid malignancy in men and the second most common cause of cancer-related death in men in North America and the European Union (EU). In 2008, over 180,000 patients will be diagnosed with prostate cancer in the United States alone and nearly 30,000 will die of this disease. Age is the single most important risk factor for the development of prostate cancer, and applies across all racial groups that have been studied. With the aging of the U.S. population, it is projected that the annual incidence of prostate cancer will double by 2025 to nearly 400,000 cases per year.

Since the introduction of prostate-specific antigen (PSA) screening in the 1990's, the proportion of patients presenting with clinically evident disease has fallen dramatically such that patients categorized as “low risk” now constitute half of new diagnoses today. PSA is used as a tumor marker to determine the presence of prostate cancer as high PSA levels are associated with prostate cancer. Despite a growing proportion of localized prostate cancer patients presenting with low-risk features such as low stage (T1) disease, greater than 90% of patients in the US still undergo definitive therapy, including prostatectomy or radiation. Only about 15% of these patients would develop metastatic disease and die from their prostate cancer, even in the absence of definitive therapy. A. Bill-Axelson, et al., J Nat'l Cancer Inst. 100(16):1144-1154 (2008). Therefore, the majority of prostate cancer patients are being over-treated.

Estimates of recurrence risk and treatment decisions in prostate cancer are currently based primarily on PSA levels and/or tumor stage. Although tumor stage has been demonstrated to have significant association with outcome sufficient to be included in pathology reports, the College of American Pathologists Consensus Statement noted that variations in approach to the acquisition, interpretation, reporting, and analysis of this information exist. C. Compton, et al., Arch Pathol Lab Med 124:979-992 (2000). As a consequence, existing pathologic staging methods have been criticized as lacking reproducibility and therefore may provide imprecise estimates of individual patient risk.

SUMMARY

This application discloses molecular assays that involve measurement of expression level(s) of one or more genes, gene subsets, microRNAs, or one or more microRNAs in combination with one or more genes or gene subsets, from a biological sample obtained from a prostate cancer patient, and analysis of the measured expression levels to provide information concerning the likelihood of cancer recurrence. For example, the likelihood of cancer recurrence could be described in terms of a score based on clinical or biochemical recurrence-free interval.

In addition, this application discloses molecular assays that involve measurement of expression level(s) of one or more genes, gene subsets, microRNAs, or one or more microRNAs in combination with one or more genes or gene subsets, from a biological sample obtained to identify a risk classification for a prostate cancer patient. For example, patients may be stratified using expression level(s) of one or more genes or microRNAs associated, positively or negatively, with cancer recurrence or death from cancer, or with a prognostic factor. In an exemplary embodiment, the prognostic factor is Gleason pattern.

The biological sample may be obtained from standard methods, including surgery, biopsy, or bodily fluids. It may comprise tumor tissue or cancer cells, and, in some cases, histologically normal tissue, e.g., histologically normal tissue adjacent the tumor tissue. In exemplary embodiments, the biological sample is positive or negative for a TMPRSS2 fusion.

In exemplary embodiments, expression level(s) of one or more genes and/or microRNAs that are associated, positively or negatively, with a particular clinical outcome in prostate cancer are used to determine prognosis and appropriate therapy. The genes disclosed herein may be used alone or arranged in functional gene subsets, such as cell adhesion/migration, immediate-early stress response, and extracellular matrix-associated. Each gene subset comprises the genes disclosed herein, as well as genes that are co-expressed with one or more of the disclosed genes. The calculation may be performed on a computer, programmed to execute the gene expression analysis. The microRNAs disclosed herein may also be used alone or in combination with any one or more of the microRNAs and/or genes disclosed.

In exemplary embodiments, the molecular assay may involve expression levels for at least two genes. The genes, or gene subsets, may be weighted according to strength of association with prognosis or tumor microenvironment. In another exemplary embodiment, the molecular assay may involve expression levels of at least one gene and at least one microRNA. The gene-microRNA combination may be selected based on the likelihood that the gene-microRNA combination functionally interact.

BRIEF DESCRIPTION OF THE DRAWING

FIG. 1 shows the distribution of clinical and pathology assessments of biopsy Gleason score, baseline PSA level, and clinical T-stage.

DEFINITIONS

Unless defined otherwise, technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which this invention belongs. Singleton et al., Dictionary of Microbiology and Molecular Biology 2nd ed., J. Wiley & Sons (New York, N.Y. 1994), and March, Advanced Organic Chemistry Reactions, Mechanisms and Structure 4th ed., John Wiley & Sons (New York, N.Y. 1992), provide one skilled in the art with a general guide to many of the terms used in the present application.

One skilled in the art will recognize many methods and materials similar or equivalent to those described herein, which could be used in the practice of the present invention. Indeed, the present invention is in no way limited to the methods and materials described herein. For purposes of the invention, the following terms are defined below.

The terms “tumor” and “lesion” as used herein, refer to all neoplastic cell growth and proliferation, whether malignant or benign, and all pre-cancerous and cancerous cells and tissues. Those skilled in the art will realize that a tumor tissue sample may comprise multiple biological elements, such as one or more cancer cells, partial or fragmented cells, tumors in various stages, surrounding histologically normal-appearing tissue, and/or macro or micro-dissected tissue.

The terms “cancer” and “cancerous” refer to or describe the physiological condition in mammals that is typically characterized by unregulated cell growth. Examples of cancer in the present disclosure include cancer of the urogenital tract, such as prostate cancer.

The “pathology” of cancer includes all phenomena that compromise the well-being of the patient. This includes, without limitation, abnormal or uncontrollable cell growth, metastasis, interference with the normal functioning of neighboring cells, release of cytokines or other secretory products at abnormal levels, suppression or aggravation of inflammatory or immunological response, neoplasia, premalignancy, malignancy, invasion of surrounding or distant tissues or organs, such as lymph nodes, etc.

As used herein, the term “prostate cancer” is used interchangeably and in the broadest sense refers to all stages and all forms of cancer arising from the tissue of the prostate gland.

According to the tumor, node, metastasis (TNM) staging system of the American Joint Committee on Cancer (AJCC), AJCC Cancer Staging Manual (7th Ed., 2010), the various stages of prostate cancer are defined as follows: Tumor: T1: clinically inapparent tumor not palpable or visible by imaging, T1a: tumor incidental histological finding in 5% or less of tissue resected, T1b: tumor incidental histological finding in more than 5% of tissue resected, T1c: tumor identified by needle biopsy; T2: tumor confined within prostate, T2a: tumor involves one half of one lobe or less, T2b: tumor involves more than half of one lobe, but not both lobes, T2c: tumor involves both lobes; T3: tumor extends through the prostatic capsule, T3a: extracapsular extension (unilateral or bilateral), T3b: tumor invades seminal vesicle(s); T4: tumor is fixed or invades adjacent structures other than seminal vesicles (bladder neck, external sphincter, rectum, levator muscles, or pelvic wall). Node: NO: no regional lymph node metastasis; N1: metastasis in regional lymph nodes. Metastasis: M0: no distant metastasis; M1: distant metastasis present.

The Gleason Grading system is used to help evaluate the prognosis of men with prostate cancer. Together with other parameters, it is incorporated into a strategy of prostate cancer staging, which predicts prognosis and helps guide therapy. A Gleason “score” or “grade” is given to prostate cancer based upon its microscopic appearance. Tumors with a low Gleason score typically grow slowly enough that they may not pose a significant threat to the patients in their lifetimes. These patients are monitored (“watchful waiting” or “active surveillance”) over time. Cancers with a higher Gleason score are more aggressive and have a worse prognosis, and these patients are generally treated with surgery (e.g., radical prostectomy) and, in some cases, therapy (e.g., radiation, hormone, ultrasound, chemotherapy). Gleason scores (or sums) comprise grades of the two most common tumor patterns. These patterns are referred to as Gleason patterns 1-5, with pattern 1 being the most well-differentiated. Most have a mixture of patterns. To obtain a Gleason score or grade, the dominant pattern is added to the second most prevalent pattern to obtain a number between 2 and 10. The Gleason Grades include: G1: well differentiated (slight anaplasia) (Gleason 2-4); G2: moderately differentiated (moderate anaplasia) (Gleason 5-6); G3-4: poorly differentiated/undifferentiated (marked anaplasia) (Gleason 7-10).

Stage groupings: Stage I: T1a N0 M0 G1; Stage II: (T1a N0 M0 G2-4) or (T1b, c, T1, T2, N0 M0 Any G); Stage III: T3 N0 M0 Any G; Stage IV: (T4 N0 M0 Any G) or (Any T N1 M0 Any G) or (Any T Any N M1 Any G).

As used herein, the term “tumor tissue” refers to a biological sample containing one or more cancer cells, or a fraction of one or more cancer cells. Those skilled in the art will recognize that such biological sample may additionally comprise other biological components, such as histologically appearing normal cells (e.g., adjacent the tumor), depending upon the method used to obtain the tumor tissue, such as surgical resection, biopsy, or bodily fluids.

As used herein, the term “AUA risk group” refers to the 2007 updated American Urological Association (AUA) guidelines for management of clinically localized prostate cancer, which clinicians use to determine whether a patient is at low, intermediate, or high risk of biochemical (PSA) relapse after local therapy.

As used herein, the term “adjacent tissue (AT)” refers to histologically “normal” cells that are adjacent a tumor. For example, the AT expression profile may be associated with disease recurrence and survival.

As used herein “non-tumor prostate tissue” refers to histologically normal-appearing tissue adjacent a prostate tumor.

Prognostic factors are those variables related to the natural history of cancer, which influence the recurrence rates and outcome of patients once they have developed cancer. Clinical parameters that have been associated with a worse prognosis include, for example, increased tumor stage, PSA level at presentation, and Gleason grade or pattern. Prognostic factors are frequently used to categorize patients into subgroups with different baseline relapse risks.

The term “prognosis” is used herein to refer to the likelihood that a cancer patient will have a cancer-attributable death or progression, including recurrence, metastatic spread, and drug resistance, of a neoplastic disease, such as prostate cancer. For example, a “good prognosis” would include long term survival without recurrence and a “bad prognosis” would include cancer recurrence.

As used herein, the term “expression level” as applied to a gene refers to the normalized level of a gene product, e.g. the normalized value determined for the RNA expression level of a gene or for the polypeptide expression level of a gene.

The term “gene product” or “expression product” are used herein to refer to the RNA (ribonucleic acid) transcription products (transcripts) of the gene, including mRNA, and the polypeptide translation products of such RNA transcripts. A gene product can be, for example, an unspliced RNA, an mRNA, a splice variant mRNA, a microRNA, a fragmented RNA, a polypeptide, a post-translationally modified polypeptide, a splice variant polypeptide, etc.

The term “RNA transcript” as used herein refers to the RNA transcription products of a gene, including, for example, mRNA, an unspliced RNA, a splice variant mRNA, a microRNA, and a fragmented RNA.

The term “microRNA” is used herein to refer to a small, non-coding, single-stranded RNA of ˜18-25 nucleotides that may regulate gene expression. For example, when associated with the RNA-induced silencing complex (RISC), the complex binds to specific mRNA targets and causes translation repression or cleavage of these mRNA sequences.

Unless indicated otherwise, each gene name used herein corresponds to the Official Symbol assigned to the gene and provided by Entrez Gene (URL: www.ncbi.nlm.nih.gov/sites/entrez) as of the filing date of this application.

The terms “correlated” and “associated” are used interchangeably herein to refer to the association between two measurements (or measured entities). The disclosure provides genes, gene subsets, microRNAs, or microRNAs in combination with genes or gene subsets, the expression levels of which are associated with tumor stage. For example, the increased expression level of a gene or microRNA may be positively correlated (positively associated) with a good or positive prognosis. Such a positive correlation may be demonstrated statistically in various ways, e.g. by a cancer recurrence hazard ratio less than one. In another example, the increased expression level of a gene or microRNA may be negatively correlated (negatively associated) with a good or positive prognosis. In that case, for example, the patient may experience a cancer recurrence.

The terms “good prognosis” or “positive prognosis” as used herein refer to a beneficial clinical outcome, such as long-term survival without recurrence. The terms “bad prognosis” or “negative prognosis” as used herein refer to a negative clinical outcome, such as cancer recurrence.

The term “risk classification” means a grouping of subjects by the level of risk (or likelihood) that the subject will experience a particular clinical outcome. A subject may be classified into a risk group or classified at a level of risk based on the methods of the present disclosure, e.g. high, medium, or low risk. A “risk group” is a group of subjects or individuals with a similar level of risk for a particular clinical outcome.

The term “long-term” survival is used herein to refer to survival for a particular time period, e.g., for at least 5 years, or for at least 10 years.

The term “recurrence” is used herein to refer to local or distant recurrence (i.e., metastasis) of cancer. For example, prostate cancer can recur locally in the tissue next to the prostate or in the seminal vesicles. The cancer may also affect the surrounding lymph nodes in the pelvis or lymph nodes outside this area. Prostate cancer can also spread to tissues next to the prostate, such as pelvic muscles, bones, or other organs. Recurrence can be determined by clinical recurrence detected by, for example, imaging study or biopsy, or biochemical recurrence detected by, for example, sustained follow-up prostate-specific antigen (PSA) levels ≥0.4 ng/mL or the initiation of salvage therapy as a result of a rising PSA level.

The term “clinical recurrence-free interval (cRFI)” is used herein as time (in months) from surgery to first clinical recurrence or death due to clinical recurrence of prostate cancer. Losses due to incomplete follow-up, other primary cancers or death prior to clinical recurrence are considered censoring events; when these occur, the only information known is that up through the censoring time, clinical recurrence has not occurred in this subject. Biochemical recurrences are ignored for the purposes of calculating cRFI.

The term “biochemical recurrence-free interval (bRFI)” is used herein to mean the time (in months) from surgery to first biochemical recurrence of prostate cancer. Clinical recurrences, losses due to incomplete follow-up, other primary cancers, or death prior to biochemical recurrence are considered censoring events.

The term “Overall Survival (OS)” is used herein to refer to the time (in months) from surgery to death from any cause. Losses due to incomplete follow-up are considered censoring events. Biochemical recurrence and clinical recurrence are ignored for the purposes of calculating OS.

The term “Prostate Cancer-Specific Survival (PCSS)” is used herein to describe the time (in years) from surgery to death from prostate cancer. Losses due to incomplete follow-up or deaths from other causes are considered censoring events. Clinical recurrence and biochemical recurrence are ignored for the purposes of calculating PCSS.

The term “upgrading” or “upstaging” as used herein refers to a change in Gleason grade from 3+3 at the time of biopsy to 3+4 or greater at the time of radical prostatectomy (RP), or Gleason grade 3+4 at the time of biopsy to 4+3 or greater at the time of RP, or seminal vessical involvement (SVI), or extracapsular involvement (ECE) at the time of RP.

In practice, the calculation of the measures listed above may vary from study to study depending on the definition of events to be considered censored.

The term “microarray” refers to an ordered arrangement of hybridizable array elements, e.g. oligonucleotide or polynucleotide probes, on a substrate.

The term “polynucleotide” generally refers to any polyribonucleotide or polydeoxribonucleotide, which may be unmodified RNA or DNA or modified RNA or DNA. Thus, for instance, polynucleotides as defined herein include, without limitation, single- and double-stranded DNA, DNA including single- and double-stranded regions, single- and double-stranded RNA, and RNA including single- and double-stranded regions, hybrid molecules comprising DNA and RNA that may be single-stranded or, more typically, double-stranded or include single- and double-stranded regions. In addition, the term “polynucleotide” as used herein refers to triple-stranded regions comprising RNA or DNA or both RNA and DNA. The strands in such regions may be from the same molecule or from different molecules. The regions may include all of one or more of the molecules, but more typically involve only a region of some of the molecules. One of the molecules of a triple-helical region often is an oligonucleotide. The term “polynucleotide” specifically includes cDNAs. The term includes DNAs (including cDNAs) and RNAs that contain one or more modified bases. Thus, DNAs or RNAs with backbones modified for stability or for other reasons, are “polynucleotides” as that term is intended herein. Moreover, DNAs or RNAs comprising unusual bases, such as inosine, or modified bases, such as tritiated bases, are included within the term “polynucleotides” as defined herein. In general, the term “polynucleotide” embraces all chemically, enzymatically and/or metabolically modified forms of unmodified polynucleotides, as well as the chemical forms of DNA and RNA characteristic of viruses and cells, including simple and complex cells.

The term “oligonucleotide” refers to a relatively short polynucleotide, including, without limitation, single-stranded deoxyribonucleotides, single- or double-stranded ribonucleotides, RNArDNA hybrids and double-stranded DNAs. Oligonucleotides, such as single-stranded DNA probe oligonucleotides, are often synthesized by chemical methods, for example using automated oligonucleotide synthesizers that are commercially available. However, oligonucleotides can be made by a variety of other methods, including in vitro recombinant DNA-mediated techniques and by expression of DNAs in cells and organisms.

The term “Ct” as used herein refers to threshold cycle, the cycle number in quantitative polymerase chain reaction (qPCR) at which the fluorescence generated within a reaction well exceeds the defined threshold, i.e. the point during the reaction at which a sufficient number of amplicons have accumulated to meet the defined threshold.

The term “Cp” as used herein refers to “crossing point.” The Cp value is calculated by determining the second derivatives of entire qPCR amplification curves and their maximum value. The Cp value represents the cycle at which the increase of fluorescence is highest and where the logarithmic phase of a PCR begins.

The terms “threshold” or “thresholding” refer to a procedure used to account for non-linear relationships between gene expression measurements and clinical response as well as to further reduce variation in reported patient scores. When thresholding is applied, all measurements below or above a threshold are set to that threshold value. Non-linear relationship between gene expression and outcome could be examined using smoothers or cubic splines to model gene expression in Cox PH regression on recurrence free interval or logistic regression on recurrence status. D. Cox, Journal of the Royal Statistical Society, Series B 34:187-220 (1972). Variation in reported patient scores could be examined as a function of variability in gene expression at the limit of quantitation and/or detection for a particular gene.

As used herein, the term “amplicon,” refers to pieces of DNA that have been synthesized using amplification techniques, such as polymerase chain reactions (PCR) and ligase chain reactions.

“Stringency” of hybridization reactions is readily determinable by one of ordinary skill in the art, and generally is an empirical calculation dependent upon probe length, washing temperature, and salt concentration. In general, longer probes require higher temperatures for proper annealing, while shorter probes need lower temperatures. Hybridization generally depends on the ability of denatured DNA to re-anneal when complementary strands are present in an environment below their melting temperature. The higher the degree of desired homology between the probe and hybridizable sequence, the higher the relative temperature which can be used. As a result, it follows that higher relative temperatures would tend to make the reaction conditions more stringent, while lower temperatures less so. For additional details and explanation of stringency of hybridization reactions, see Ausubel et al., Current Protocols in Molecular Biology (Wiley Interscience Publishers, 1995).

“Stringent conditions” or “high stringency conditions”, as defined herein, typically: (1) employ low ionic strength and high temperature for washing, for example 0.015 M sodium chloride/0.0015 M sodium citrate/0.1% sodium dodecyl sulfate at 50° C.; (2) employ during hybridization a denaturing agent, such as formamide, for example, 50% (v/v) formamide with 0.1% bovine serum albumin/0.1% Ficoll/0.1% polyvinylpyrrolidone/50 mM sodium phosphate buffer at pH 6.5 with 750 mM sodium chloride, 75 mM sodium citrate at 42° C.; or (3) employ 50% formamide, 5×SSC (0.75 M NaCl, 0.075 M sodium citrate), 50 mM sodium phosphate (pH 6.8), 0.1% sodium pyrophosphate, 5×Denhardt's solution, sonicated salmon sperm DNA (50 μg/ml), 0.1% SDS, and 10% dextran sulfate at 42° C., with washes at 42° C. in 0.2×SSC (sodium chloride/sodium citrate) and 50% formamide, followed by a high-stringency wash consisting of 0.1×SSC containing EDTA at 55° C.

“Moderately stringent conditions” may be identified as described by Sambrook et al., Molecular Cloning: A Laboratory Manual, New York: Cold Spring Harbor Press, 1989, and include the use of washing solution and hybridization conditions (e.g., temperature, ionic strength and % SDS) less stringent that those described above. An example of moderately stringent conditions is overnight incubation at 37° C. in a solution comprising: 20% formamide, 5×SSC (150 mM NaCl, 15 mM trisodium citrate), 50 mM sodium phosphate (pH 7.6), 5×Denhardt's solution, 10% dextran sulfate, and 20 mg/ml denatured sheared salmon sperm DNA, followed by washing the filters in 1×SSC at about 37-50° C. The skilled artisan will recognize how to adjust the temperature, ionic strength, etc. as necessary to accommodate factors such as probe length and the like.

The terms “splicing” and “RNA splicing” are used interchangeably and refer to RNA processing that removes introns and joins exons to produce mature mRNA with continuous coding sequence that moves into the cytoplasm of an eukaryotic cell.

The terms “co-express” and “co-expressed”, as used herein, refer to a statistical correlation between the amounts of different transcript sequences across a population of different patients. Pairwise co-expression may be calculated by various methods known in the art, e.g., by calculating Pearson correlation coefficients or Spearman correlation coefficients. Co-expressed gene cliques may also be identified using graph theory. An analysis of co-expression may be calculated using normalized expression data. A gene is said to be co-expressed with a particular disclosed gene when the expression level of the gene exhibits a Pearson correlation coefficient greater than or equal to 0.6.

A “computer-based system” refers to a system of hardware, software, and data storage medium used to analyze information. The minimum hardware of a patient computer-based system comprises a central processing unit (CPU), and hardware for data input, data output (e.g., display), and data storage. An ordinarily skilled artisan can readily appreciate that any currently available computer-based systems and/or components thereof are suitable for use in connection with the methods of the present disclosure. The data storage medium may comprise any manufacture comprising a recording of the present information as described above, or a memory access device that can access such a manufacture.

To “record” data, programming or other information on a computer readable medium refers to a process for storing information, using any such methods as known in the art. Any convenient data storage structure may be chosen, based on the means used to access the stored information. A variety of data processor programs and formats can be used for storage, e.g. word processing text file, database format, etc.

A “processor” or “computing means” references any hardware and/or software combination that will perform the functions required of it. For example, a suitable processor may be a programmable digital microprocessor such as available in the form of an electronic controller, mainframe, server or personal computer (desktop or portable). Where the processor is programmable, suitable programming can be communicated from a remote location to the processor, or previously saved in a computer program product (such as a portable or fixed computer readable storage medium, whether magnetic, optical or solid state device based). For example, a magnetic medium or optical disk may carry the programming, and can be read by a suitable reader communicating with each processor at its corresponding station.

As used herein, the terms “active surveillance” and “watchful waiting” mean closely monitoring a patient's condition without giving any treatment until symptoms appear or change. For example, in prostate cancer, watchful waiting is usually used in older men with other medical problems and early-stage disease.

As used herein, the term “surgery” applies to surgical methods undertaken for removal of cancerous tissue, including pelvic lymphadenectomy, radical prostatectomy, transurethral resection of the prostate (TURP), excision, dissection, and tumor biopsy/removal. The tumor tissue or sections used for gene expression analysis may have been obtained from any of these methods.

As used herein, the term “therapy” includes radiation, hormonal therapy, cryosurgery, chemotherapy, biologic therapy, and high-intensity focused ultrasound.

As used herein, the term “TMPRSS fusion” and “TMPRSS2 fusion” are used interchangeably and refer to a fusion of the androgen-driven TMPRSS2 gene with the ERG oncogene, which has been demonstrated to have a significant association with prostate cancer. S. Perner, et al., Urologe A. 46(7):754-760 (2007); S. A. Narod, et al., Br J Cancer 99(6):847-851 (2008). As used herein, positive TMPRSS fusion status indicates that the TMPRSS fusion is present in a tissue sample, whereas negative TMPRSS fusion status indicates that the TMPRSS fusion is not present in a tissue sample. Experts skilled in the art will recognize that there are numerous ways to determine TMPRSS fusion status, such as real-time, quantitative PCR or high-throughput sequencing. See, e.g., K. Mertz, et al., Neoplasis 9(3):200-206 (2007); C. Maher, Nature 458(7234):97-101 (2009).

Gene Expression Methods Using Genes, Gene Subsets, and MicroRNAs

The present disclosure provides molecular assays that involve measurement of expression level(s) of one or more genes, gene subsets, microRNAs, or one or more microRNAs in combination with one or more genes or gene subsets, from a biological sample obtained from a prostate cancer patient, and analysis of the measured expression levels to provide information concerning the likelihood of cancer recurrence.

The present disclosure further provides methods to classify a prostate tumor based on expression level(s) of one or more genes and/or microRNAs. The disclosure further provides genes and/or microRNAs that are associated, positively or negatively, with a particular prognostic outcome. In exemplary embodiments, the clinical outcomes include cRFI and bRFI. In another embodiment, patients may be classified in risk groups based on the expression level(s) of one or more genes and/or microRNAs that are associated, positively or negatively, with a prognostic factor. In an exemplary embodiment, that prognostic factor is Gleason pattern.

Various technological approaches for determination of expression levels of the disclosed genes and microRNAs are set forth in this specification, including, without limitation, RT-PCR, microarrays, high-throughput sequencing, serial analysis of gene expression (SAGE) and Digital Gene Expression (DGE), which will be discussed in detail below. In particular aspects, the expression level of each gene or microRNA may be determined in relation to various features of the expression products of the gene including exons, introns, protein epitopes and protein activity.

The expression level(s) of one or more genes and/or microRNAs may be measured in tumor tissue. For example, the tumor tissue may obtained upon surgical removal or resection of the tumor, or by tumor biopsy. The tumor tissue may be or include histologically “normal” tissue, for example histologically “normal” tissue adjacent to a tumor. The expression level of genes and/or microRNAs may also be measured in tumor cells recovered from sites distant from the tumor, for example circulating tumor cells, body fluid (e.g., urine, blood, blood fraction, etc.).

The expression product that is assayed can be, for example, RNA or a polypeptide. The expression product may be fragmented. For example, the assay may use primers that are complementary to target sequences of an expression product and could thus measure full transcripts as well as those fragmented expression products containing the target sequence. Further information is provided in Table A (inserted in specification prior to claims).

The RNA expression product may be assayed directly or by detection of a cDNA product resulting from a PCR-based amplification method, e.g., quantitative reverse transcription polymerase chain reaction (qRT-PCR). (See e.g., U.S. Pat. No. 7,587,279). Polypeptide expression product may be assayed using immunohistochemistry (IHC). Further, both RNA and polypeptide expression products may also be is assayed using microarrays.

Clinical Utility

Prostate cancer is currently diagnosed using a digital rectal exam (DRE) and Prostate-specific antigen (PSA) test. If PSA results are high, patients will generally undergo a prostate tissue biopsy. The pathologist will review the biopsy samples to check for cancer cells and determine a Gleason score. Based on the Gleason score, PSA, clinical stage, and other factors, the physician must make a decision whether to monitor the patient, or treat the patient with surgery and therapy.

At present, clinical decision-making in early stage prostate cancer is governed by certain histopathologic and clinical factors. These include: (1) tumor factors, such as clinical stage (e.g. T1, T2), PSA level at presentation, and Gleason grade, that are very strong prognostic factors in determining outcome; and (2) host factors, such as age at diagnosis and co-morbidity. Because of these factors, the most clinically useful means of stratifying patients with localized disease according to prognosis has been through multifactorial staging, using the clinical stage, the serum PSA level, and tumor grade (Gleason grade) together. In the 2007 updated American Urological Association (AUA) guidelines for management of clinically localized prostate cancer, these parameters have been grouped to determine whether a patient is at low, intermediate, or high risk of biochemical (PSA) relapse after local therapy. I. Thompson, et al., Guideline for the management of clinically localized prostate cancer, J Urol. 177(6):2106-31 (2007).

Although such classifications have proven to be helpful in distinguishing patients with localized disease who may need adjuvant therapy after surgery/radiation, they have less ability to discriminate between indolent cancers, which do not need to be treated with local therapy, and aggressive tumors, which require local therapy. In fact, these algorithms are of increasingly limited use for deciding between conservative management and definitive therapy because the bulk of prostate cancers diagnosed in the PSA screening era now present with clinical stage T1c and PSA ≤10 ng/mL.

Patients with T1 prostate cancer have disease that is not clinically apparent but is discovered either at transurethral resection of the prostate (TURP, T1a, T1b) or at biopsy performed because of an elevated PSA (>4 ng/mL, T1c). Approximately 80% of the cases presenting in 2007 are clinical T1 at diagnosis. In a Scandinavian trial, OS at 10 years was 85% for patients with early stage prostate cancer (T1/T2) and Gleason score ≤7, after radical prostatectomy.

Patients with T2 prostate cancer have disease that is clinically evident and is organ confined; patients with T3 tumors have disease that has penetrated the prostatic capsule and/or has invaded the seminal vesicles. It is known from surgical series that clinical staging underestimates pathological stage, so that about 20% of patients who are clinically T2 will be pT3 after prostatectomy. Most of patients with T2 or T3 prostate cancer are treated with local therapy, either prostatectomy or radiation. The data from the Scandinavian trial suggest that for T2 patients with Gleason grade ≤7, the effect of prostatectomy on survival is at most 5% at 10 years; the majority of patients do not benefit from surgical treatment at the time of diagnosis. For T2 patients with Gleason >7 or for T3 patients, the treatment effect of prostatectomy is assumed to be significant but has not been determined in randomized trials. It is known that these patients have a significant risk (10-30%) of recurrence at 10 years after local treatment, however, there are no prospective randomized trials that define the optimal local treatment (radical prostatectomy, radiation) at diagnosis, which patients are likely to benefit from neo-adjuvant/adjuvant androgen deprivation therapy, and whether treatment (androgen deprivation, chemotherapy) at the time of biochemical failure (elevated PSA) has any clinical benefit.

Accurately determining Gleason scores from needle biopsies presents several technical challenges. First, interpreting histology that is “borderline” between Gleason pattern is highly subjective, even for urologic pathologists. Second, incomplete biopsy sampling is yet another reason why the “predicted” Gleason score on biopsy does not always correlate with the actual “observed” Gleason score of the prostate cancer in the gland itself. Hence, the accuracy of Gleason scoring is dependent upon not only the expertise of the pathologist reading the slides, but also on the completeness and adequacy of the prostate biopsy sampling strategy. T. Stamey, Urology 45:2-12 (1995). The gene/microRNA expression assay and associated information provided by the practice of the methods disclosed herein provide a molecular assay method to facilitate optimal treatment decision-making in early stage prostate cancer. An exemplary embodiment provides genes and microRNAs, the expression levels of which are associated (positively or negatively) with prostate cancer recurrence. For example, such a clinical tool would enable physicians to identify T2/T3 patients who are likely to recur following definitive therapy and need adjuvant treatment.

In addition, the methods disclosed herein may allow physicians to classify tumors, at a molecular level, based on expression level(s) of one or more genes and/or microRNAs that are significantly associated with prognostic factors, such as Gleason pattern and TMPRSS fusion status. These methods would not be impacted by the technical difficulties of intra-patient variability, histologically determining Gleason pattern in biopsy samples, or inclusion of histologically normal appearing tissue adjacent to tumor tissue. Multi-analyte gene/microRNA expression tests can be used to measure the expression level of one or more genes and/or microRNAs involved in each of several relevant physiologic processes or component cellular characteristics. The methods disclosed herein may group the genes and/or microRNAs. The grouping of genes and microRNAs may be performed at least in part based on knowledge of the contribution of those genes and/or microRNAs according to physiologic functions or component cellular characteristics, such as in the groups discussed above. Furthermore, one or more microRNAs may be combined with one or moregenes. The gene-microRNA combination may be selected based on the likelihood that the gene-microRNA combination functionally interact. The formation of groups (or gene subsets), in addition, can facilitate the mathematical weighting of the contribution of various expression levels to cancer recurrence. The weighting of a gene/microRNA group representing a physiological process or component cellular characteristic can reflect the contribution of that process or characteristic to the pathology of the cancer and clinical outcome.

Optionally, the methods disclosed may be used to classify patients by risk, for example risk of recurrence. Patients can be partitioned into subgroups (e.g., tertiles or quartiles) and the values chosen will define subgroups of patients with respectively greater or lesser risk.

The utility of a disclosed gene marker in predicting prognosis may not be unique to that marker. An alternative marker having an expression pattern that is parallel to that of a disclosed gene may be substituted for, or used in addition to, that co-expressed gene or microRNA. Due to the co-expression of such genes or microRNAs, substitution of expression level values should have little impact on the overall utility of the test. The closely similar expression patterns of two genes or microRNAs may result from involvement of both genes or microRNAs in the same process and/or being under common regulatory control in prostate tumor cells. The present disclosure thus contemplates the use of such co-expressed genes, gene subsets, or microRNAs as substitutes for, or in addition to, genes of the present disclosure.

Methods of Assaying Expression Levels of a Gene Product

The methods and compositions of the present disclosure will employ, unless otherwise indicated, conventional techniques of molecular biology (including recombinant techniques), microbiology, cell biology, and biochemistry, which are within the skill of the art. Exemplary techniques are explained fully in the literature, such as, “Molecular Cloning: A Laboratory Manual”, 2nd edition (Sambrook et al., 1989); “Oligonucleotide Synthesis” (M. J. Gait, ed., 1984); “Animal Cell Culture” (R. I. Freshney, ed., 1987); “Methods in Enzymology” (Academic Press, Inc.); “Handbook of Experimental Immunology”, 4th edition (D. M. Weir & C. C. Blackwell, eds., Blackwell Science Inc., 1987); “Gene Transfer Vectors for Mammalian Cells” (J. M. Miller & M. P. Calos, eds., 1987); “Current Protocols in Molecular Biology” (F. M. Ausubel et al., eds., 1987); and “PCR: The Polymerase Chain Reaction”, (Mullis et al., eds., 1994).

Methods of gene expression profiling include methods based on hybridization analysis of polynucleotides, methods based on sequencing of polynucleotides, and proteomics-based methods. Exemplary methods known in the art for the quantification of RNA expression in a sample include northern blotting and in situ hybridization (Parker & Barnes, Methods in Molecular Biology 106:247-283 (1999)); RNAse protection assays (Hod, Biotechniques 13:852-854 (1992)); and PCR-based methods, such as reverse transcription PCT (RT-PCR) (Weis et al., Trends in Genetics 8:263-264 (1992)). Antibodies may be employed that can recognize sequence-specific duplexes, including DNA duplexes, RNA duplexes, and DNA-RNA hybrid duplexes or DNA-protein duplexes. Representative methods for sequencing-based gene expression analysis include Serial Analysis of Gene Expression (SAGE), and gene expression analysis by massively parallel signature sequencing (MPSS).

Reverse Transcriptase PCR (RT-PCR)

Typically, mRNA or microRNA is isolated from a test sample. The starting material is typically total RNA isolated from a human tumor, usually from a primary tumor. Optionally, normal tissues from the same patient can be used as an internal control. Such normal tissue can be histologically-appearing normal tissue adjacent a tumor. mRNA or microRNA can be extracted from a tissue sample, e.g., from a sample that is fresh, frozen (e.g. fresh frozen), or paraffin-embedded and fixed (e.g. formalin-fixed).

General methods for mRNA and microRNA extraction are well known in the art and are disclosed in standard textbooks of molecular biology, including Ausubel et al., Current Protocols of Molecular Biology, John Wiley and Sons (1997). Methods for RNA extraction from paraffin embedded tissues are disclosed, for example, in Rupp and Locker, Lab Invest. 56:A67 (1987), and De Andres et al., BioTechniques 18:42044 (1995). In particular, RNA isolation can be performed using a purification kit, buffer set and protease from commercial manufacturers, such as Qiagen, according to the manufacturer's instructions. For example, total RNA from cells in culture can be isolated using Qiagen RNeasy mini-columns. Other commercially available RNA isolation kits include MasterPure™ Complete DNA and RNA Purification Kit (EPICENTRE®, Madison, Wis.), and Paraffin Block RNA Isolation Kit (Ambion, Inc.). Total RNA from tissue samples can be isolated using RNA Stat-60 (Tel-Test). RNA prepared from tumor can be isolated, for example, by cesium chloride density gradient centrifugation.

The sample containing the RNA is then subjected to reverse transcription to produce cDNA from the RNA template, followed by exponential amplification in a PCR reaction. The two most commonly used reverse transcriptases are avilo myeloblastosis virus reverse transcriptase (AMV-RT) and Moloney murine leukemia virus reverse transcriptase (MMLV-RT). The reverse transcription step is typically primed using specific primers, random hexamers, or oligo-dT primers, depending on the circumstances and the goal of expression profiling. For example, extracted RNA can be reverse-transcribed using a GeneAmp RNA PCR kit (Perkin Elmer, CA, USA), following the manufacturer's instructions. The derived cDNA can then be used as a template in the subsequent PCR reaction.

PCR-based methods use a thermostable DNA-dependent DNA polymerase, such as a Taq DNA polymerase. For example, TaqMan® PCR typically utilizes the 5′-nuclease activity of Taq or Tth polymerase to hydrolyze a hybridization probe bound to its target amplicon, but any enzyme with equivalent 5′ nuclease activity can be used. Two oligonucleotide primers are used to generate an amplicon typical of a PCR reaction product. A third oligonucleotide, or probe, can be designed to facilitate detection of a nucleotide sequence of the amplicon located between the hybridization sites the two PCR primers. The probe can be detectably labeled, e.g., with a reporter dye, and can further be provided with both a fluorescent dye, and a quencher fluorescent dye, as in a Taqman® probe configuration. Where a Taqman® probe is used, during the amplification reaction, the Taq DNA polymerase enzyme cleaves the probe in a template-dependent manner. The resultant probe fragments disassociate in solution, and signal from the released reporter dye is free from the quenching effect of the second fluorophore. One molecule of reporter dye is liberated for each new molecule synthesized, and detection of the unquenched reporter dye provides the basis for quantitative interpretation of the data.

TaqMan® RT-PCR can be performed using commercially available equipment, such as, for example, high-throughput platforms such as the ABI PRISM 7700 Sequence Detection System® (Perkin-Elmer-Applied Biosystems, Foster City, Calif., USA), or Lightcycler (Roche Molecular Biochemicals, Mannheim, Germany). In a preferred embodiment, the procedure is run on a LightCycler® 480 (Roche Diagnostics) real-time PCR system, which is a microwell plate-based cycler platform.

5′-Nuclease assay data are commonly initially expressed as a threshold cycle (“C_(T)”). Fluorescence values are recorded during every cycle and represent the amount of product amplified to that point in the amplification reaction. The threshold cycle (C_(T)) is generally described as the point when the fluorescent signal is first recorded as statistically significant. Alternatively, data may be expressed as a crossing point (“Cp”). The Cp value is calculated by determining the second derivatives of entire qPCR amplification curves and their maximum value. The Cp value represents the cycle at which the increase of fluorescence is highest and where the logarithmic phase of a PCR begins.

To minimize errors and the effect of sample-to-sample variation, RT-PCR is usually performed using an internal standard. The ideal internal standard gene (also referred to as a reference gene) is expressed at a quite constant level among cancerous and non-cancerous tissue of the same origin (i.e., a level that is not significantly different among normal and cancerous tissues), and is not significantly affected by the experimental treatment (i.e., does not exhibit a significant difference in expression level in the relevant tissue as a result of exposure to chemotherapy), and expressed at a quite constant level among the same tissue taken from different patients. For example, reference genes useful in the methods disclosed herein should not exhibit significantly different expression levels in cancerous prostate as compared to normal prostate tissue. RNAs frequently used to normalize patterns of gene expression are mRNAs for the housekeeping genes glyceraldehyde-3-phosphate-dehydrogenase (GAPDH) and (3-actin. Exemplary reference genes used for normalization comprise one or more of the following genes: AAMP, ARF1, ATP5E, CLTC, GPS1, and PGK1. Gene expression measurements can be normalized relative to the mean of one or more (e.g., 2, 3, 4, 5, or more) reference genes. Reference-normalized expression measurements can range from 2 to 15, where a one unit increase generally reflects a 2-fold increase in RNA quantity.

Real time PCR is compatible both with quantitative competitive PCR, where internal competitor for each target sequence is used for normalization, and with quantitative comparative PCR using a normalization gene contained within the sample, or a housekeeping gene for RT-PCR. For further details see, e.g. Held et al., Genome Research 6:986-994 (1996).

The steps of a representative protocol for use in the methods of the present disclosure use fixed, paraffin-embedded tissues as the RNA source. For example, mRNA isolation, purification, primer extension and amplification can be performed according to methods available in the art. (see, e.g., Godfrey et al. J. Molec. Diagnostics 2: 84-91 (2000); Specht et al., Am. J. Pathol. 158: 419-29 (2001)). Briefly, a representative process starts with cutting about 10 μm thick sections of paraffin-embedded tumor tissue samples. The RNA is then extracted, and protein and DNA depleted from the RNA-containing sample. After analysis of the RNA concentration, RNA is reverse transcribed using gene specific primers followed by RT-PCR to provide for cDNA amplification products.

Design of Intron-Based PCR Primers and Probes

PCR primers and probes can be designed based upon exon or intron sequences present in the mRNA transcript of the gene of interest. Primer/probe design can be performed using publicly available software, such as the DNA BLAT software developed by Kent, W. J., Genome Res. 12(4):656-64 (2002), or by the BLAST software including its variations.

Where necessary or desired, repetitive sequences of the target sequence can be masked to mitigate non-specific signals. Exemplary tools to accomplish this include the Repeat Masker program available on-line through the Baylor College of Medicine, which screens DNA sequences against a library of repetitive elements and returns a query sequence in which the repetitive elements are masked. The masked intron sequences can then be used to design primer and probe sequences using any commercially or otherwise publicly available primer/probe design packages, such as Primer Express (Applied Biosystems); MGB assay-by-design (Applied Biosystems); Primer3 (Steve Rozen and Helen J. Skaletsky (2000) Primer3 on the WWW for general users and for biologist programmers. See S. Rrawetz, S. Misener, Bioinformatics Methods and Protocols: Methods in Molecular Biology, pp. 365-386 (Humana Press).

Other factors that can influence PCR primer design include primer length, melting temperature (Tm), and G/C content, specificity, complementary primer sequences, and 3′-end sequence. In general, optimal PCR primers are generally 17-30 bases in length, and contain about 20-80%, such as, for example, about 50-60% G+C bases, and exhibit Tm's between 50 and 80° C., e.g. about 50 to 70° C.

For further guidelines for PCR primer and probe design see, e.g. Dieffenbach, C W. et al, “General Concepts for PCR Primer Design” in: PCR Primer, A Laboratory Manual, Cold Spring Harbor Laboratory Press, New York, 1995, pp. 133-155; Innis and Gelfand, “Optimization of PCRs” in: PCR Protocols, A Guide to Methods and Applications, CRC Press, London, 1994, pp. 5-11; and Plasterer, T.N. Primerselect: Primer and probe design. Methods Mol. Biol. 70:520-527 (1997), the entire disclosures of which are hereby expressly incorporated by reference.

Table A provides further information concerning the primer, probe, and amplicon sequences associated with the Examples disclosed herein.

MassARRAY® System

In MassARRAY-based methods, such as the exemplary method developed by Sequenom, Inc. (San Diego, Calif.) following the isolation of RNA and reverse transcription, the obtained cDNA is spiked with a synthetic DNA molecule (competitor), which matches the targeted cDNA region in all positions, except a single base, and serves as an internal standard. The cDNA/competitor mixture is PCR amplified and is subjected to a post-PCR shrimp alkaline phosphatase (SAP) enzyme treatment, which results in the dephosphorylation of the remaining nucleotides. After inactivarion of the alkaline phosphatase, the PCR products from the competitor and cDNA are subjected to primer extension, which generates distinct mass signals for the competitor- and cDNA-derives PCR products. After purification, these products are dispensed on a chip array, which is pre-loaded with components needed for analysis with matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) analysis. The cDNA present in the reaction is then quantified by analyzing the ratios of the peak areas in the mass spectrum generated. For further details see, e.g. Ding and Cantor, Proc. Natl. Acad. Sci. USA 100:3059-3064 (2003).

Other PCR-Based Methods

Further PCR-based techniques that can find use in the methods disclosed herein include, for example, BeadArray® technology (Illumina, San Diego, Calif.; Oliphant et al., Discovery of Markers for Disease (Supplement to Biotechniques), June 2002; Ferguson et al., Analytical Chemistry 72:5618 (2000)); BeadsArray for Detection of Gene Expression® (BADGE), using the commercially available LuminexlOO LabMAP® system and multiple color-coded microspheres (Luminex Corp., Austin, Tex.) in a rapid assay for gene expression (Yang et al., Genome Res. 11:1888-1898 (2001)); and high coverage expression profiling (HiCEP) analysis (Fukumura et al., Nucl. Acids. Res. 31(16) e94 (2003).

Microarrays

Expression levels of a gene or microArray of interest can also be assessed using the microarray technique. In this method, polynucleotide sequences of interest (including cDNAs and oligonucleotides) are arrayed on a substrate. The arrayed sequences are then contacted under conditions suitable for specific hybridization with detectably labeled cDNA generated from RNA of a test sample. As in the RT-PCR method, the source of RNA typically is total RNA isolated from a tumor sample, and optionally from normal tissue of the same patient as an internal control or cell lines. RNA can be extracted, for example, from frozen or archived paraffin-embedded and fixed (e.g. formalin-fixed) tissue samples.

For example, PCR amplified inserts of cDNA clones of a gene to be assayed are applied to a substrate in a dense array. Usually at least 10,000 nucleotide sequences are applied to the substrate. For example, the microarrayed genes, immobilized on the microchip at 10,000 elements each, are suitable for hybridization under stringent conditions. Fluorescently labeled cDNA probes may be generated through incorporation of fluorescent nucleotides by reverse transcription of RNA extracted from tissues of interest. Labeled cDNA probes applied to the chip hybridize with specificity to each spot of DNA on the array. After washing under stringent conditions to remove non-specifically bound probes, the chip is scanned by confocal laser microscopy or by another detection method, such as a CCD camera. Quantitation of hybridization of each arrayed element allows for assessment of corresponding RNA abundance.

With dual color fluorescence, separately labeled cDNA probes generated from two sources of RNA are hybridized pair wise to the array. The relative abundance of the transcripts from the two sources corresponding to each specified gene is thus determined simultaneously. The miniaturized scale of the hybridization affords a convenient and rapid evaluation of the expression pattern for large numbers of genes. Such methods have been shown to have the sensitivity required to detect rare transcripts, which are expressed at a few copies per cell, and to reproducibly detect at least approximately two-fold differences in the expression levels (Schena et at, Proc. Natl. Acad. ScL USA 93(2):106-149 (1996)). Microarray analysis can be performed by commercially available equipment, following manufacturer's protocols, such as by using the Affymetrix GenChip® technology, or Incyte's microarray technology.

Serial Analysis of Gene Expression (SAGE)

Serial analysis of gene expression (SAGE) is a method that allows the simultaneous and quantitative analysis of a large number of gene transcripts, without the need of providing an individual hybridization probe for each transcript. First, a short sequence tag (about 10-14 bp) is generated that contains sufficient information to uniquely identify a transcript, provided that the tag is obtained from a unique position within each transcript. Then, many transcripts are linked together to form long serial molecules, that can be sequenced, revealing the identity of the multiple tags simultaneously. The expression pattern of any population of transcripts can be quantitatively evaluated by determining the abundance of individual tags, and identifying the gene corresponding to each tag. For more details see, e.g. Velculescu et al., Science 270:484-487 (1995); and Velculescu et al., Cell 88:243-51 (1997).

Gene Expression Analysis by Nucleic Acid Sequencing

Nucleic acid sequencing technologies are suitable methods for analysis of gene expression. The principle underlying these methods is that the number of times a cDNA sequence is detected in a sample is directly related to the relative expression of the RNA corresponding to that sequence. These methods are sometimes referred to by the term Digital Gene Expression (DGE) to reflect the discrete numeric property of the resulting data. Early methods applying this principle were Serial Analysis of Gene Expression (SAGE) and Massively Parallel Signature Sequencing (MPSS). See, e.g., S. Brenner, et al., Nature Biotechnology 18(6):630-634 (2000). More recently, the advent of “next-generation” sequencing technologies has made DGE simpler, higher throughput, and more affordable. As a result, more laboratories are able to utilize DGE to screen the expression of more genes in more individual patient samples than previously possible. See, e.g., J. Marioni, Genome Research 18(9):1509-1517 (2008); R. Morin, Genome Research 18(4):610-621 (2008); A. Mortazavi, Nature Methods 5(7):621-628 (2008); N. Cloonan, Nature Methods 5(7):613-619 (2008).

Isolating RNA from Body Fluids

Methods of isolating RNA for expression analysis from blood, plasma and serum (see, e.g., K. Enders, et al., Clin Chem 48, 1647-53 (2002) (and references cited therein) and from urine (see, e.g., R. Boom, et al., J Clin Microbiol. 28, 495-503 (1990) and references cited therein) have been described.

Immunohistochemistry

Immunohistochemistry methods are also suitable for detecting the expression levels of genes and applied to the method disclosed herein. Antibodies (e.g., monoclonal antibodies) that specifically bind a gene product of a gene of interest can be used in such methods. The antibodies can be detected by direct labeling of the antibodies themselves, for example, with radioactive labels, fluorescent labels, hapten' labels such as, biotin, or an enzyme such as horse radish peroxidase or alkaline phosphatase. Alternatively, unlabeled primary antibody can be used in conjunction with a labeled secondary antibody specific for the primary antibody. Immunohistochemistry protocols and kits are well known in the art and are commercially available.

Proteomics

The term “proteome” is defined as the totality of the proteins present in a sample (e.g. tissue, organism, or cell culture) at a certain point of time. Proteomics includes, among other things, study of the global changes of protein expression in a sample (also referred to as “expression proteomics”). Proteomics typically includes the following steps: (1) separation of individual proteins in a sample by 2-D gel electrophoresis (2-D PAGE); (2) identification of the individual proteins recovered from the gel, e.g. my mass spectrometry or N-terminal sequencing, and (3) analysis of the data using bioinformatics.

General Description of the mRNA/microRNA Isolation, Purification and Amplification

The steps of a representative protocol for profiling gene expression using fixed, paraffin-embedded tissues as the RNA source, including mRNA or microRNA isolation, purification, primer extension and amplification are provided in various published journal articles. (See, e.g., T. E. Godfrey, et al, J. Molec. Diagnostics 2: 84-91 (2000); K. Specht et al., Am. J. Pathol. 158: 419-29 (2001), M. Cronin, et al., Am J Pathol 164:35-42 (2004)). Briefly, a representative process starts with cutting a tissue sample section (e.g. about 10 μm thick sections of a paraffin-embedded tumor tissue sample). The RNA is then extracted, and protein and DNA are removed. After analysis of the RNA concentration, RNA repair is performed if desired. The sample can then be subjected to analysis, e.g., by reverse transcribed using gene specific promoters followed by RT-PCR.

Statistical Analysis of Expression Levels in Identification of Genes and MicroRNAs

One skilled in the art will recognize that there are many statistical methods that may be used to determine whether there is a significant relationship between a parameter of interest (e.g., recurrence) and expression levels of a marker gene/microRNA as described here. In an exemplary embodiment, the present invention provides a stratified cohort sampling design (a form of case-control sampling) using tissue and data from prostate cancer patients. Selection of specimens was stratified by T stage (T1, T2), year cohort (<1993, ≥1993), and prostatectomy Gleason Score (low/intermediate, high). All patients with clinical recurrence were selected and a sample of patients who did not experience a clinical recurrence was selected. For each patient, up to two enriched tumor specimens and one normal-appearing tissue sample was assayed.

All hypothesis tests were reported using two-sided p-values. To investigate if there is a significant relationship of outcomes (clinical recurrence-free interval (cRFI), biochemical recurrence-free interval (bRFI), prostate cancer-specific survival (PCSS), and overall survival (OS)) with individual genes and/or microRNAs, demographic or clinical covariates Cox Proportional Hazards (PH) models using maximum weighted pseudo partial-likelihood estimators were used and p-values from Wald tests of the null hypothesis that the hazard ratio (HR) is one are reported. To investigate if there is a significant relationship between individual genes and/or microRNAs and Gleason pattern of a particular sample, ordinal logistic regression models using maximum weighted likelihood methods were used and p-values from Wald tests of the null hypothesis that the odds ratio (OR) is one are reported.

Coexpression Analysis

The present disclosure provides a method to determine tumor stage based on the expression of staging genes, or genes that co-express with particular staging genes. To perform particular biological processes, genes often work together in a concerted way, i.e. they are co-expressed. Co-expressed gene groups identified for a disease process like cancer can serve as biomarkers for tumor status and disease progression. Such co-expressed genes can be assayed in lieu of, or in addition to, assaying of the staging gene with which they are co-expressed.

In an exemplary embodiment, the joint correlation of gene expression levels among prostate cancer specimens under study may be assessed. For this purpose, the correlation structures among genes and specimens may be examined through hierarchical cluster methods. This information may be used to confirm that genes that are known to be highly correlated in prostate cancer specimens cluster together as expected. Only genes exhibiting a nominally significant (unadjusted p<0.05) relationship with cRFI in the univariate Cox PH regression analysis will be included in these analyses.

One skilled in the art will recognize that many co-expression analysis methods now known or later developed will fall within the scope and spirit of the present invention. These methods may incorporate, for example, correlation coefficients, co-expression network analysis, clique analysis, etc., and may be based on expression data from RT-PCR, microarrays, sequencing, and other similar technologies. For example, gene expression clusters can be identified using pair-wise analysis of correlation based on Pearson or Spearman correlation coefficients. (See, e.g., Pearson K. and Lee A., Biometrika 2, 357 (1902); C. Spearman, Amer. J. Psychol 15:72-101 (1904); J. Myers, A. Well, Research Design and Statistical Analysis, p. 508 (2nd Ed., 2003).)

Normalization of Expression Levels

The expression data used in the methods disclosed herein can be normalized. Normalization refers to a process to correct for (normalize away), for example, differences in the amount of RNA assayed and variability in the quality of the RNA used, to remove unwanted sources of systematic variation in Ct or Cp measurements, and the like. With respect to RT-PCR experiments involving archived fixed paraffin embedded tissue samples, sources of systematic variation are known to include the degree of RNA degradation relative to the age of the patient sample and the type of fixative used to store the sample. Other sources of systematic variation are attributable to laboratory processing conditions.

Assays can provide for normalization by incorporating the expression of certain normalizing genes, which do not significantly differ in expression levels under the relevant conditions. Exemplary normalization genes disclosed herein include housekeeping genes. (See, e.g., E. Eisenberg, et al., Trends in Genetics 19(7):362-365 (2003).) Normalization can be based on the mean or median signal (Ct or Cp) of all of the assayed genes or a large subset thereof (global normalization approach). In general, the normalizing genes, also referred to as reference genes should be genes that are known not to exhibit significantly different expression in prostate cancer as compared to non-cancerous prostate tissue, and are not significantly affected by various sample and process conditions, thus provide for normalizing away extraneous effects.

In exemplary embodiments, one or more of the following genes are used as references by which the mRNA or microRNA expression data is normalized: AAMP, ARF1, ATP5E, CLTC, GPS1, and PGK1. In another exemplary embodiment, one or more of the following microRNAs are used as references by which the expression data of microRNAs are normalized: hsa-miR-106a; hsa-miR-146b-5p; hsa-miR-191; hsa-miR-19b; and hsa-miR-92a. The calibrated weighted average C_(T) or Cp measurements for each of the prognostic and predictive genes or microRNAs may be normalized relative to the mean of five or more reference genes or microRNAs.

Those skilled in the art will recognize that normalization may be achieved in numerous ways, and the techniques described above are intended only to be exemplary, not exhaustive.

Standardization of Expression Levels

The expression data used in the methods disclosed herein can be standardized. Standardization refers to a process to effectively put all the genes or microRNAs on a comparable scale. This is performed because some genes or microRNAs will exhibit more variation (a broader range of expression) than others. Standardization is performed by dividing each expression value by its standard deviation across all samples for that gene or microRNA. Hazard ratios are then interpreted as the relative risk of recurrence per 1 standard deviation increase in expression.

Kits of the Invention

The materials for use in the methods of the present invention are suited for preparation of kits produced in accordance with well-known procedures. The present disclosure thus provides kits comprising agents, which may include gene (or microRNA)-specific or gene (or microRNA)-selective probes and/or primers, for quantifying the expression of the disclosed genes or microRNAs for predicting prognostic outcome or response to treatment. Such kits may optionally contain reagents for the extraction of RNA from tumor samples, in particular fixed paraffin-embedded tissue samples and/or reagents for RNA amplification. In addition, the kits may optionally comprise the reagent(s) with an identifying description or label or instructions relating to their use in the methods of the present invention. The kits may comprise containers (including microliter plates suitable for use in an automated implementation of the method), each with one or more of the various materials or reagents (typically in concentrated form) utilized in the methods, including, for example, chromatographic columns, pre-fabricated microarrays, buffers, the appropriate nucleotide triphosphates (e.g., dATP, dCTP, dGTP and dTTP; or rATP, rCTP, rGTP and UTP), reverse transcriptase, DNA polymerase, RNA polymerase, and one or more probes and primers of the present invention (e.g., appropriate length poly(T) or random primers linked to a promoter reactive with the RNA polymerase). Mathematical algorithms used to estimate or quantify prognostic or predictive information are also properly potential components of kits.

Reports

The methods of this invention, when practiced for commercial diagnostic purposes, generally produce a report or summary of information obtained from the herein-described methods. For example, a report may include information concerning expression levels of one or more genes and/or microRNAs, classification of the tumor or the patient's risk of recurrence, the patient's likely prognosis or risk classification, clinical and pathologic factors, and/or other information. The methods and reports of this invention can further include storing the report in a database. The method can create a record in a database for the subject and populate the record with data. The report may be a paper report, an auditory report, or an electronic record. The report may be displayed and/or stored on a computing device (e.g., handheld device, desktop computer, smart device, website, etc.). It is contemplated that the report is provided to a physician and/or the patient. The receiving of the report can further include establishing a network connection to a server computer that includes the data and report and requesting the data and report from the server computer.

Computer Program

The values from the assays described above, such as expression data, can be calculated and stored manually. Alternatively, the above-described steps can be completely or partially performed by a computer program product. The present invention thus provides a computer program product including a computer readable storage medium having a computer program stored on it. The program can, when read by a computer, execute relevant calculations based on values obtained from analysis of one or more biological sample from an individual (e.g., gene expression levels, normalization, standardization, thresholding, and conversion of values from assays to a score and/or text or graphical depiction of tumor stage and related information). The computer program product has stored therein a computer program for performing the calculation.

The present disclosure provides systems for executing the program described above, which system generally includes: a) a central computing environment; b) an input device, operatively connected to the computing environment, to receive patient data, wherein the patient data can include, for example, expression level or other value obtained from an assay using a biological sample from the patient, or microarray data, as described in detail above; c) an output device, connected to the computing environment, to provide information to a user (e.g., medical personnel); and d) an algorithm executed by the central computing environment (e.g., a processor), where the algorithm is executed based on the data received by the input device, and wherein the algorithm calculates an expression score, thresholding, or other functions described herein. The methods provided by the present invention may also be automated in whole or in part.

All aspects of the present invention may also be practiced such that a limited number of additional genes and/or microRNAs that are co-expressed or functionally related with the disclosed genes, for example as evidenced by statistically meaningful Pearson and/or Spearman correlation coefficients, are included in a test in addition to and/or in place of disclosed genes.

Having described the invention, the same will be more readily understood through reference to the following Examples, which are provided by way of illustration, and are not intended to limit the invention in any way.

EXAMPLES Example 1: RNA Yield and Gene Expression Profiles in Prostate Cancer Biopsy Cores

Clinical tools based on prostate needle core biopsies are needed to guide treatment planning at diagnosis for men with localized prostate cancer. Limiting tissue in needle core biopsy specimens poses significant challenges to the development of molecular diagnostic tests. This study examined RNA extraction yields and gene expression profiles using an RT-PCR assay to characterize RNA from manually micro-dissected fixed paraffin embedded (FPE) prostate cancer needle biopsy cores. It also investigated the association of RNA yields and gene expression profiles with Gleason score in these specimens.

Patients and Samples

This study determined the feasibility of gene expression profile analysis in prostate cancer needle core biopsies by evaluating the quantity and quality of RNA extracted from fixed paraffin-embedded (FPE) prostate cancer needle core biopsy specimens. Forty-eight (48) formalin-fixed blocks from prostate needle core biopsy specimens were used for this study. Classification of specimens was based on interpretation of the Gleason score (2005 Int'l Society of Urological Pathology Consensus Conference) and percentage tumor (<33%, 33-66%, >66%) involvement as assessed by pathologists.

TABLE 1 Distribution of cases Gleason score ~<33% ~33-66% ~>66% Category Tumor Tumor Tumor Low (≤6) 5 5 6 Intermediate (7) 5 5 6 High (8, 9, 10) 5 5 6 Total 15 15 18

Assay Methods

Fourteen (14) serial 5 μm unstained sections from each FPE tissue block were included in the study. The first and last sections for each case were H&E stained and histologically reviewed to confirm the presence of tumor and for tumor enrichment by manual micro-dissection.

RNA from enriched tumor samples was extracted using a manual RNA extraction process. RNA was quantitated using the RiboGreen® assay and tested for the presence of genomic DNA contamination. Samples with sufficient RNA yield and free of genomic DNA tested for gene expression levels of a 24-gene panel of reference and cancer-related genes using quantitative RT-PCR. The expression was normalized to the average of 6 reference genes (AAMP, ARF1, ATP5E, CLTC, EEF1A1, and GPX1).

Statistical Methods

Descriptive statistics and graphical displays were used to summarize standard pathology metrics and gene expression, with stratification for Gleason Score category and percentage tumor involvement category. Ordinal logistic regression was used to evaluate the relationship between gene expression and Gleason Score category.

Results

The RNA yield per unit surface area ranged from 16 to 2406 ng/mm2. Higher RNA yield was observed in samples with higher percent tumor involvement (p=0.02) and higher Gleason score (p=0.01). RNA yield was sufficient (>200 ng) in 71% of cases to permit 96-well RT-PCR, with 87% of cases having >100 ng RNA yield. The study confirmed that gene expression from prostate biopsies, as measured by qRT-PCR, was comparable to FPET samples used in commercial molecular assays for breast cancer. In addition, it was observed that greater biopsy RNA yields are found with higher Gleason score and higher percent tumor involvement. Nine genes were identified as significantly associated with Gleason score (p<0.05) and there was a large dynamic range observed for many test genes.

Example 2: Gene Expression Analysis for Genes Associated with Prognosis in Prostate Cancer

Patients and Samples

Approximately 2600 patients with clinical stage T1/T2 prostate cancer treated with radical prostatectomy (RP) at the Cleveland Clinic between 1987 and 2004 were identified. Patients were excluded from the study design if they received neo-adjuvant and/or adjuvant therapy, if pre-surgical PSA levels were missing, or if no tumor block was available from initial diagnosis. 127 patients with clinical recurrence and 374 patients without clinical recurrence after radical prostatectomy were randomly selected using a cohort sampling design. The specimens were stratified by T stage (T1, T2), year cohort (<1993, ≥1993), and prostatectomy Gleason score (low/intermediate, high). Of the 501 sampled patients, 51 were excluded for insufficient tumor; 7 were excluded due to clinical ineligibility; 2 were excluded due to poor quality of gene expression data; and 10 were excluded because primary Gleason pattern was unavailable. Thus, this gene expression study included tissue and data from 111 patients with clinical recurrence and 330 patients without clinical recurrence after radical prostatectomies performed between 1987 and 2004 for treatment of early stage (T1, T2) prostate cancer.

Two fixed paraffin embedded (FPE) tissue specimens were obtained from prostate tumor specimens in each patient. The sampling method (sampling method A or B) depended on whether the highest Gleason pattern is also the primary Gleason pattern. For each specimen selected, the invasive cancer cells were at least 5.0 mm in dimension, except in the instances of pattern 5, where 2.2 mm was accepted. Specimens were spatially distinct where possible.

TABLE 2 Sampling Methods Sampling Method A Sampling Method B For patients whose prostatectomy For patients whose prostatectomy primary Gleason pattern is also primary Gleason pattern is not the highest Gleason pattern the highest Gleason pattern Specimen 1 (A1) = Specimen 1 (B1) = primary Gleason pattern highest Gleason pattern Select and mark largest focus Select highest Gleason pattern (greatest cross-sectional area) tissue from spatially distinct area of primary Gleason pattern from specimen B2, if tissue. Invasive cancer area possible. Invasive cancer area ≥5.0 mm. at least 5.0 mm if selecting secondary pattern, at least 2.2 mm if selecting Gleason pattern 5. Specimen 2 (A2) = Specimen 2 (B2) = secondary Gleason pattern primary Gleason pattern Select and mark secondary Select largest focus Gleason pattern tissue from (greatest cross-sectional area) spatially distinct area from of primary Gleason pattern tissue. specimen A1. Invasive cancer Invasive cancer area ≥5.0 mm. area ≥5.0 mm.

Histologically normal appearing tissue (NAT) adjacent to the tumor specimen (also referred to in these Examples as “non-tumor tissue”) was also evaluated. Adjacent tissue was collected 3 mm from the tumor to 3 mm from the edge of the FPET block. NAT was preferentially sampled adjacent to the primary Gleason pattern. In cases where there was insufficient NAT adjacent to the primary Gleason pattern, then NAT was sampled adjacent to the secondary or highest Gleason pattern (A2 or B1) per the method set forth in Table 2. Six (6) 10 μm sections with beginning H&E at 5 μm and ending unstained slide at 5 μm were prepared from each fixed paraffin-embedded tumor (FPET) block included in the study. All cases were histologically reviewed and manually micro-dissected to yield two enriched tumor samples and, where possible, one normal tissue sample adjacent to the tumor specimen.

Assay Method

In this study, RT-PCR analysis was used to determine RNA expression levels for 738 genes and chromosomal rearrangements (e.g., TMPRSS2-ERG fusion or other ETS family genes) in prostate cancer tissue and surrounding NAT in patients with early-stage prostate cancer treated with radical prostatectomy.

The samples were quantified using the RiboGreen assay and a subset tested for presence of genomic DNA contamination. Samples were taken into reverse transcription (RT) and quantitative polymerase chain reaction (qPCR). All analyses were conducted on reference-normalized gene expression levels using the average of the of replicate well crossing point (CP) values for the 6 reference genes (AAMP, ARF1, ATP5E, CLTC, GPS1, PGK1).

Statistical Analysis and Results

Primary statistical analyses involved 111 patients with clinical recurrence and 330 patients without clinical recurrence after radical prostatectomy for early-stage prostate cancer stratified by T-stage (T1, T2), year cohort (<1993, ≥1993), and prostatectomy Gleason score (low/intermediate, high). Gleason score categories are defined as follows: low (Gleason score ≤6), intermediate (Gleason score=7), and high (Gleason score ≥8). A patient was included in a specified analysis if at least one sample for that patient was evaluable. Unless otherwise stated, all hypothesis tests were reported using two-sided p-values. The method of Storey was applied to the resulting set of p-values to control the false discovery rate (FDR) at 20%. J. Storey, R. Tibshirani, Estimating the Positive False Discovery Rate Under Dependence, with Applications to DNA Microarrays, Dept. of Statistics, Stanford Univ. (2001).

Analysis of gene expression and recurrence-free interval was based on univariate Cox Proportional Hazards (PH) models using maximum weighted pseudo-partial-likelihood estimators for each evaluable gene in the gene list (727 test genes and 5 reference genes). P-values were generated using Wald tests of the null hypothesis that the hazard ratio (HR) is one. Both unadjusted p-values and the q-value (smallest FDR at which the hypothesis test in question is rejected) were reported. Un-adjusted p-values <0.05 were considered statistically significant. Since two tumor specimens were selected for each patient, this analysis was performed using the 2 specimens from each patient as follows: (1) analysis using the primary Gleason pattern specimen from each patient (Specimens A1 and B2 as described in Table 2); (2) analysis using the highest Gleason pattern specimen from each patient (Specimens A1 and B1 as described in Table 2).

Analysis of gene expression and Gleason pattern (3, 4, 5) was based on univariate ordinal logistic regression models using weighted maximum likelihood estimators for each gene in the gene list (727 test genes and 5 reference genes). P-values were generated using a Wald test of the null hypothesis that the odds ratio (OR) is one. Both unadjusted p-values and the q-value (smallest FDR at which the hypothesis test in question is rejected) were reported. Un-adjusted p-values <0.05 were considered statistically significant. Since two tumor specimens were selected for each patient, this analysis was performed using the 2 specimens from each patient as follows: (1) analysis using the primary Gleason pattern specimen from each patient (Specimens A1 and B2 as described in Table 2); (2) analysis using the highest Gleason pattern specimen from each patient (Specimens A1 and B1 as described in Table 2).

It was determined whether there is a significant relationship between cRFI and selected demographic, clinical, and pathology variables, including age, race, clinical tumor stage, pathologic tumor stage, location of selected tumor specimens within the prostate (peripheral versus transitional zone), PSA at the time of surgery, overall Gleason score from the radical prostatectomy, year of surgery, and specimen Gleason pattern. Separately for each demographic or clinical variable, the relationship between the clinical covariate and cRFI was modeled using univariate Cox PH regression using weighted pseudo partial-likelihood estimators and a p-value was generated using Wald's test of the null hypothesis that the hazard ratio (HR) is one. Covariates with unadjusted p-values <0.2 may have been included in the covariate-adjusted analyses.

It was determined whether there was a significant relationship between each of the individual cancer-related genes and cRFI after controlling for important demographic and clinical covariates. Separately for each gene, the relationship between gene expression and cRFI was modeled using multivariate Cox PH regression using weighted pseudo partial-likelihood estimators including important demographic and clinical variables as covariates. The independent contribution of gene expression to the prediction of cRFI was tested by generating a p-value from a Wald test using a model that included clinical covariates for each nodule (specimens as defined in Table 2). Un-adjusted p-values <0.05 were considered statistically significant.

Tables 3A and 3B provide genes significantly associated (p<0.05), positively or negatively, with Gleason pattern in the primary and/or highest Gleason pattern. Increased expression of genes in Table 3A is positively associated with higher Gleason score, while increased expression of genes in Table 3B are negatively associated with higher Gleason score.

TABLE 3A Gene significantly (p < 0.05) associated with Gleason pattern for all specimens in the primary Gleason pattern or highest Gleason pattern odds ratio (OR) >1.0 (Increased expression is positively associated with higher Gleason Score) Primary Pattern Highest Pattern Official Symbol OR p-value OR p-value ALCAM 1.73 <.001 1.36 0.009 ANLN 1.35 0.027 APOC1 1.47 0.005 1.61 <.001 APOE 1.87 <.001 2.15 <.001 ASAP2 1.53 0.005 ASPN 2.62 <.001 2.13 <.001 ATP5E 1.35 0.035 AURKA 1.44 0.010 AURKB 1.59 <.001 1.56 <.001 BAX 1.43 0.006 BGN 2.58 <.001 2.82 <.001 BIRC5 1.45 0.003 1.79 <.001 BMP6 2.37 <.001 1.68 <.001 BMPR1B 1.58 0.002 BRCA2 1.45 0.013 BUB1 1.73 <.001 1.57 <.001 CACNA1D 1.31 0.045 1.31 0.033 CADPS 1.30 0.023 CCNB1 1.43 0.023 CCNE2 1.52 0.003 1.32 0.035 CD276 2.20 <.001 1.83 <.001 CD68 1.36 0.022 CDC20 1.69 <.001 1.95 <.001 CDC6 1.38 0.024 1.46 <.001 CDH11 1.30 0.029 CDKN2B 1.55 0.001 1.33 0.023 CDKN2C 1.62 <.001 1.52 <.001 CDKN3 1.39 0.010 1.50 0.002 CENPF 1.96 <.001 1.71 <.001 CHRAC1 1.34 0.022 CLDN3 1.37 0.029 COL1A1 2.23 <.001 2.22 <.001 COL1A2 1.42 0.005 COL3A1 1.90 <.001 2.13 <.001 COL8A1 1.88 <.001 2.35 <.001 CRISP3 1.33 0.040 1.26 0.050 CTHRC1 2.01 <.001 1.61 <.001 CTNND2 1.48 0.007 1.37 0.011 DAPK1 1.44 0.014 DIAPH1 1.34 0.032 1.79 <.001 DIO2 1.56 0.001 DLL4 1.38 0.026 1.53 <.001 ECE1 1.54 0.012 1.40 0.012 ENY2 1.35 0.046 1.35 0.012 EZH2 1.39 0.040 F2R 2.37 <.001 2.60 <.001 FAM49B 1.57 0.002 1.33 0.025 FAP 2.36 <.001 1.89 <.001 FCGR3A 2.10 <.001 1.83 <.001 GNPTAB 1.78 <.001 1.54 <.001 GSK3B 1.39 0.018 HRAS 1.62 0.003 HSD17B4 2.91 <.001 1.57 <.001 HSPA8 1.48 0.012 1.34 0.023 IFI30 1.64 <.001 1.45 0.013 IGFBP3 1.29 0.037 IL11 1.52 0.001 1.31 0.036 INHBA 2.55 <.001 2.30 <.001 ITGA4 1.35 0.028 JAG1 1.68 <.001 1.40 0.005 KCNN2 1.50 0.004 KCTD12 1.38 0.012 KHDRBS3 1.85 <.001 1.72 <.001 KIF4A 1.50 0.010 1.50 <.001 KLK14 1.49 0.001 1.35 <.001 KPNA2 1.68 0.004 1.65 0.001 KRT2 1.33 0.022 KRT75 1.27 0.028 LAMC1 1.44 0.029 LAPTM5 1.36 0.025 1.31 0.042 LTBP2 1.42 0.023 1.66 <.001 MANF 1.34 0.019 MAOA 1.55 0.003 1.50 <.001 MAP3K5 1.55 0.006 1.44 0.001 MDK 1.47 0.013 1.29 0.041 MDM2 1.31 0.026 MELK 1.64 <.001 1.64 <.001 MMP11 2.33 <.001 1.66 <.001 MYBL2 1.41 0.007 1.54 <.001 MYO6 1.32 0.017 NETO2 1.36 0.018 NOX4 1.84 <.001 1.73 <.001 NPM1 1.68 0.001 NRIP3 1.36 0.009 NRP1 1.80 0.001 1.36 0.019 OSM 1.33 0.046 PATE1 1.38 0.032 PECAM1 1.38 0.021 1.31 0.035 PGD 1.56 0.010 PLK1 1.51 0.004 1.49 0.002 PLOD2 1.29 0.027 POSTN 1.70 0.047 1.55 0.006 PPP3CA 1.38 0.037 1.37 0.006 PTK6 1.45 0.007 1.53 <.001 PTTG1 1.51 <.001 RAB31 1.31 0.030 RAD21 2.05 <.001 1.38 0.020 RAD51 1.46 0.002 1.26 0.035 RAF1 1.46 0.017 RALBP1 1.37 0.043 RHOC 1.33 0.021 ROBO2 1.52 0.003 1.41 0.006 RRM2 1.77 <.001 1.50 <.001 SAT1 1.67 0.002 1.61 <.001 SDC1 1.66 0.001 1.46 0.014 SEC14L1 1.53 0.003 1.62 <.001 SESN3 1.76 <.001 1.45 <.001 SFRP4 2.69 <.001 2.03 <.001 SHMT2 1.69 0.007 1.45 0.003 SKIL 1.46 0.005 SOX4 1.42 0.016 1.27 0.031 SPARC 1.40 0.024 1.55 <.001 SPINK1 1.29 0.002 SPP1 1.51 0.002 1.80 <.001 TFDP1 1.48 0.014 THBS2 1.87 <.001 1.65 <.001 THY1 1.58 0.003 1.64 <.001 TK1 1.79 <.001 1.42 0.001 TOP2A 2.30 <.001 2.01 <.001 TPD52 1.95 <.001 1.30 0.037 TPX2 2.12 <.001 1.86 <.001 TYMP 1.36 0.020 TYMS 1.39 0.012 1.31 0.036 UBE2C 1.66 <.001 1.65 <.001 UBE2T 1.59 <.001 1.33 0.017 UGDH 1.28 0.049 UGT2B15 1.46 0.001 1.25 0.045 UHRF1 1.95 <.001 1.62 <.001 VDR 1.43 0.010 1.39 0.018 WNT5A 1.54 0.001 1.44 0.013

TABLE 3B Gene significantly (p < 0.05) associated with Gleason pattern for all specimens in the primary Gleason pattern or highest Gleason pattern odds ratio (OR) < 1.0 (Increased expression is negatively associated with higher Gleason score) Table 3B Primary Pattern Highest Pattern Official Symbol OR p-value OR p-value ABCA5 0.78 0.041 ABCG2 0.65 0.001 0.72 0.012 ACOX2 0.44 <.001 0.53 <.001 ADH5 0.45 <.001 0.42 <.001 AFAP1 0.79 0.038 AIG1 0.77 0.024 AKAP1 0.63 0.002 AKR1C1 0.66 0.003 0.63 <.001 AKT3 0.68 0.006 0.77 0.010 ALDH1A2 0.28 <.001 0.33 <.001 ALKBH3 0.77 0.040 0.77 0.029 AMPD3 0.67 0.007 ANPEP 0.68 0.008 0.59 <.001 ANXA2 0.72 0.018 APC 0.69 0.002 AXIN2 0.46 <.001 0.54 <.001 AZGP1 0.52 <.001 0.53 <.001 BIK 0.69 0.006 0.73 0.003 BIN1 0.43 <.001 0.61 <.001 BTG3 0.79 0.030 BTRC 0.48 <.001 0.62 <.001 C7 0.37 <.001 0.55 <.001 CADM1 0.56 <.001 0.69 0.001 CAV1 0.58 0.002 0.70 0.009 CAV2 0.65 0.029 CCNH 0.67 0.006 0.77 0.048 CD164 0.59 0.003 0.57 <.001 CDC25B 0.77 0.035 CDH1 0.66 <.001 CDK2 0.71 0.003 CDKN1C 0.58 <.001 0.57 <.001 CDS2 0.69 0.002 CHN1 0.66 0.002 COL6A1 0.44 <.001 0.66 <.001 COL6A3 0.66 0.006 CSRP1 0.42 0.006 CTGF 0.74 0.043 CTNNA1 0.70 <.001 0.83 0.018 CTNNB1 0.70 0.019 CTNND1 0.75 0.028 CUL1 0.74 0.011 CXCL12 0.54 <.001 0.74 0.006 CYP3A5 0.52 <.001 0.66 0.003 CYR61 0.64 0.004 0.68 0.005 DDR2 0.57 0.002 0.73 0.004 DES 0.34 <.001 0.58 <.001 DLGAP1 0.54 <.001 0.62 <.001 DNM3 0.67 0.004 DPP4 0.41 <.001 0.53 <.001 DPT 0.28 <.001 0.48 <.001 DUSP1 0.59 <.001 0.63 <.001 EDNRA 0.64 0.004 0.74 0.008 EGF 0.71 0.012 EGR1 0.59 <.001 0.67 0.009 EGR3 0.72 0.026 0.71 0.025 EIF5 0.76 0.025 ELK4 0.58 0.001 0.70 0.008 ENPP2 0.66 0.002 0.70 0.005 EPHA3 0.65 0.006 EPHB2 0.60 <.001 0.78 0.023 EPHB4 0.75 0.046 0.73 0.006 ERBB3 0.76 0.040 0.75 0.013 ERBB4 0.74 0.023 ERCC1 0.63 <.001 0.77 0.016 FAAH 0.67 0.003 0.71 0.010 FAM107A 0.35 <.001 0.59 <.001 FAM13C 0.37 <.001 0.48 <.001 FAS 0.73 0.019 0.72 0.008 FGF10 0.53 <.001 0.58 <.001 FGF7 0.52 <.001 0.59 <.001 FGFR2 0.60 <.001 0.59 <.001 FKBP5 0.70 0.039 0.68 0.003 FLNA 0.39 <.001 0.56 <.001 FLNC 0.33 <.001 0.52 <.001 FOS 0.58 <.001 0.66 0.005 FOXO1 0.57 <.001 0.67 <.001 FOXQ1 0.74 0.023 GADD45B 0.62 0.002 0.71 0.010 GHR 0.62 0.002 0.72 0.009 GNRH1 0.74 0.049 0.75 0.026 GPM6B 0.48 <.001 0.68 <.001 GPS1 0.68 0.003 GSN 0.46 <.001 0.77 0.027 GSTM1 0.44 <.001 0.62 <.001 GSTM2 0.29 <.001 0.49 <.001 HGD 0.77 0.020 HIRIP3 0.75 0.034 HK1 0.48 <.001 0.66 0.001 HLF 0.42 <.001 0.55 <.001 HNF1B 0.67 0.006 0.74 0.010 HPS1 0.66 0.001 0.65 <.001 HSP90AB1 0.75 0.042 HSPA5 0.70 0.011 HSPB2 0.52 <.001 0.70 0.004 IGF1 0.35 <.001 0.59 <.001 IGF2 0.48 <.001 0.70 0.005 IGFBP2 0.61 <.001 0.77 0.044 IGFBP5 0.63 <.001 IGFBP6 0.45 <.001 0.64 <.001 IL6ST 0.55 0.004 0.63 <.001 ILK 0.40 <.001 0.57 <.001 ING5 0.56 <.001 0.78 0.033 ITGA1 0.56 0.004 0.61 <.001 ITGA3 0.78 0.035 ITGA5 0.71 0.019 0.75 0.017 ITGA7 0.37 <.001 0.52 <.001 ITGB3 0.63 0.003 0.70 0.005 ITPR1 0.46 <.001 0.64 <.001 ITPR3 0.70 0.013 ITSN1 0.62 0.001 JUN 0.48 <.001 0.60 <.001 JUNB 0.72 0.025 KIT 0.51 <.001 0.68 0.007 KLC1 0.58 <.001 KLK1 0.69 0.028 0.66 0.003 KLK2 0.60 <.001 KLK3 0.63 <.001 0.69 0.012 KRT15 0.56 <.001 0.60 <.001 KRT18 0.74 0.034 KRT5 0.64 <.001 0.62 <.001 LAMA4 0.47 <.001 0.73 0.010 LAMB3 0.73 0.018 0.69 0.003 LGALS3 0.59 0.003 0.54 <.001 LIG3 0.75 0.044 MAP3K7 0.66 0.003 0.79 0.031 MCM3 0.73 0.013 0.80 0.034 MGMT 0.61 0.001 0.71 0.007 MGST1 0.75 0.017 MLXIP 0.70 0.013 MMP2 0.57 <.001 0.72 0.010 MMP7 0.69 0.009 MPPED2 0.70 0.009 0.59 <.001 MSH6 0.78 0.046 MTA1 0.69 0.007 MTSS1 0.55 <.001 0.54 <.001 MYBPC1 0.45 <.001 0.45 <.001 NCAM1 0.51 <.001 0.65 <.001 NCAPD3 0.42 <.001 0.53 <.001 NCOR2 0.68 0.002 NDUFS5 0.66 0.001 0.70 0.013 NEXN 0.48 <.001 0.62 <.001 NFAT5 0.55 <.001 0.67 0.001 NFKBIA 0.79 0.048 NRG1 0.58 0.001 0.62 0.001 OLFML3 0.42 <.001 0.58 <.001 OMD 0.67 0.004 0.71 0.004 OR51E2 0.65 <.001 0.76 0.007 PAGE4 0.27 <.001 0.46 <.001 PCA3 0.68 0.004 PCDHGB7 0.70 0.025 0.65 <.001 PGF 0.62 0.001 PGR 0.63 0.028 PHTF2 0.69 0.033 PLP2 0.54 <.001 0.71 0.003 PPAP2B 0.41 <.001 0.54 <.001 PPP1R12A 0.48 <.001 0.60 <.001 PRIMA1 0.62 0.003 0.65 <.001 PRKAR1B 0.70 0.009 PRKAR2B 0.79 0.038 PRKCA 0.37 <.001 0.55 <.001 PRKCB 0.47 <.001 0.56 <.001 PTCH1 0.70 0.021 PTEN 0.66 0.010 0.64 <.001 PTGER3 0.76 0.015 PTGS2 0.70 0.013 0.68 0.005 PTH1R 0.48 <.001 PTK2B 0.67 0.014 0.69 0.002 PYCARD 0.72 0.023 RAB27A 0.76 0.017 RAGE 0.77 0.040 0.57 <.001 RARB 0.66 0.002 0.69 0.002 RECK 0.65 <.001 RHOA 0.73 0.043 RHOB 0.61 0.005 0.62 <.001 RND3 0.63 0.006 0.66 <.001 SDHC 0.69 0.002 SEC23A 0.61 <.001 0.74 0.010 SEMA3A 0.49 <.001 0.55 <.001 SERPINA3 0.70 0.034 0.75 0.020 SH3RF2 0.33 <.001 0.42 <.001 SLC22A3 0.23 <.001 0.37 <.001 SMAD4 0.33 <.001 0.39 <.001 SMARCC2 0.62 0.003 0.74 0.008 SMO 0.53 <.001 0.73 0.009 SORBS1 0.40 <.001 0.55 <.001 SPARCL1 0.42 <.001 0.63 <.001 SRD5A2 0.28 <.001 0.37 <.001 STS 0.52 <.001 0.63 <.001 STAT5A 0.60 <.001 0.75 0.020 STAT5B 0.54 <.001 0.65 <.001 STS 0.78 0.035 SUMO1 0.75 0.017 0.71 0.002 SVIL 0.45 <.001 0.62 <.001 TARP 0.72 0.017 TGFB1I1 0.37 <.001 0.53 <.001 TGFB2 0.61 0.025 0.59 <.001 TGFB3 0.46 <.001 0.60 <.001 TIMP2 0.62 0.001 TIMP3 0.55 <.001 0.76 0.019 TMPRSS2 0.71 0.014 TNF 0.65 0.010 TNFRSF10A 0.71 0.014 0.74 0.010 TNFRSF10B 0.74 0.030 0.73 0.016 TNFSF10 0.69 0.004 TP53 0.73 0.011 TP63 0.62 <.001 0.68 0.003 TPM1 0.43 <.001 0.47 <.001 TPM2 0.30 <.001 0.47 <.001 TPP2 0.58 <.001 0.69 0.001 TRA2A 0.71 0.006 TRAF3IP2 0.50 <.001 0.63 <.001 TRO 0.40 <.001 0.59 <.001 TRPC6 0.73 0.030 TRPV6 0.80 0.047 VCL 0.44 <.001 0.55 <.001 VEGFB 0.73 0.029 VIM 0.72 0.013 VTI1B 0.78 0.046 WDR19 0.65 <.001 WFDC1 0.50 <.001 0.72 0.010 YY1 0.75 0.045 ZFHX3 0.52 <.001 0.54 <.001 ZFP36 0.65 0.004 0.69 0.012 ZNF827 0.59 <.001 0.69 0.004

To identify genes associated with recurrence (cRFI, bRFI) in the primary and the highest Gleason pattern, each of 727 genes were analyzed in univariate models using specimens A1 and B2 (see Table 2, above). Tables 4A and 4B provide genes that were associated, positively or negatively, with cRFI and/or bRFI in the primary and/or highest Gleason pattern. Increased expression of genes in Table 4A is negatively associated with good prognosis, while increased expression of genes in Table 4B is positively associated with good prognosis.

TABLE 4A Genes significantly (p < 0.05) associated with cRFI or bRFI in the primary Gleason pattern or highest Gleason pattern with hazard ratio (HR) > 1.0 (increased expression is negatively associated with good prognosis) cRFI cRFI bRFI bRFI Official Primary Pattern Highest Pattern Primary Pattern Highest Pattern Symbol HR p-value HR p-value HR p-value HR p-value AKR1C3 1.304 0.022 1.312 0.013 ANLN 1.379 0.002 1.579 <.001 1.465 <.001 1.623 <.001 AQP2 1.184 0.027 1.276 <.001 ASAP2 1.442 0.006 ASPN 2.272 <.001 2.106 <.001 1.861 <.001 1.895 <.001 ATP5E 1.414 0.013 1.538 <.001 BAG5 1.263 0.044 BAX 1.332 0.026 1.327 0.012 1.438 0.002 BGN 1.947 <.001 2.061 <.001 1.339 0.017 BIRC5 1.497 <.001 1.567 <.001 1.478 <.001 1.575 <.001 BMP6 1.705 <.001 2.016 <.001 1.418 0.004 1.541 <.001 BMPR1B 1.401 0.013 1.325 0.016 BRCA2 1.259 0.007 BUB1 1.411 <.001 1.435 <.001 1.352 <.001 1.242 0.002 CADPS 1.387 0.009 1.294 0.027 CCNB1 1.296 0.016 1.376 0.002 CCNE2 1.468 <.001 1.649 <.001 1.729 <.001 1.563 <.001 CD276 1.678 <.001 1.832 <.001 1.581 <.001 1.385 0.002 CDC20 1.547 <.001 1.671 <.001 1.446 <.001 1.540 <.001 CDC6 1.400 0.003 1.290 0.030 1.403 0.002 1.276 0.019 CDH7 1.403 0.003 1.413 0.002 CDKN2B 1.569 <.001 1.752 <.001 1.333 0.017 1.347 0.006 CDKN2C 1.612 <.001 1.780 <.001 1.323 0.005 1.335 0.004 CDKN3 1.384 <.001 1.255 0.024 1.285 0.003 1.216 0.028 CENPF 1.578 <.001 1.692 <.001 1.740 <.001 1.705 <.001 CKS2 1.390 0.007 1.418 0.005 1.291 0.018 CLTC 1.368 0.045 COL1A1 1.873 <.001 2.103 <.001 1.491 <.001 1.472 <.001 COL1A2 1.462 0.001 COL3A1 1.827 <.001 2.005 <.001 1.302 0.012 1.298 0.018 COL4A1 1.490 0.002 1.613 <.001 COL8A1 1.692 <.001 1.926 <.001 1.307 0.013 1.317 0.010 CRISP3 1.425 0.001 1.467 <.001 1.242 0.045 CTHRC1 1.505 0.002 2.025 <.001 1.425 0.003 1.369 0.005 CTNND2 1.412 0.003 CXCR4 1.312 0.023 1.355 0.008 DDIT4 1.543 <.001 1.763 <.001 DYNLL1 1.290 0.039 1.201 0.004 EIF3H 1.428 0.012 ENY2 1.361 0.014 1.392 0.008 1.371 0.001 EZH2 1.311 0.010 F2R 1.773 <.001 1.695 <.001 1.495 <.001 1.277 0.018 FADD 1.292 0.018 FAM171B 1.285 0.036 FAP 1.455 0.004 1.560 0.001 1.298 0.022 1.274 0.038 FASN 1.263 0.035 FCGR3A 1.654 <.001 1.253 0.033 1.350 0.007 FGF5 1.219 0.030 GNPTAB 1.388 0.007 1.503 0.003 1.355 0.005 1.434 0.002 GPR68 1.361 0.008 GREM1 1.470 0.003 1.716 <.001 1.421 0.003 1.316 0.017 HDAC1 1.290 0.025 HDAC9 1.395 0.012 HRAS 1.424 0.006 1.447 0.020 HSD17B4 1.342 0.019 1.282 0.026 1.569 <.001 1.390 0.002 HSPA8 1.290 0.034 IGFBP3 1.333 0.022 1.442 0.003 1.253 0.040 1.323 0.005 INHBA 2.368 <.001 2.765 <.001 1.466 0.002 1.671 <.001 JAG1 1.359 0.006 1.367 0.005 1.259 0.024 KCNN2 1.361 0.011 1.413 0.005 1.312 0.017 1.281 0.030 KHDRBS3 1.387 0.006 1.601 <.001 1.573 <.001 1.353 0.006 KIAA0196 1.249 0.037 KIF4A 1.212 0.016 1.149 0.040 1.278 0.003 KLK14 1.167 0.023 1.180 0.007 KPNA2 1.425 0.009 1.353 0.005 1.305 0.019 KRT75 1.164 0.028 LAMA3 1.327 0.011 LAMB1 1.347 0.019 LAMC1 1.555 0.001 1.310 0.030 1.349 0.014 LIMS1 1.275 0.022 LOX 1.358 0.003 1.410 <.001 LTBP2 1.396 0.009 1.656 <.001 1.278 0.022 LUM 1.315 0.021 MANF 1.660 <.001 1.323 0.011 MCM2 1.345 0.011 1.387 0.014 MCM6 1.307 0.023 1.352 0.008 1.244 0.039 MELK 1.293 0.014 1.401 <.001 1.501 <.001 1.256 0.012 MMP11 1.680 <.001 1.474 <.001 1.489 <.001 1.257 0.030 MRPL13 1.260 0.025 MSH2 1.295 0.027 MYBL2 1.664 <.001 1.670 <.001 1.399 <.001 1.431 <.001 MYO6 1.301 0.033 NETO2 1.412 0.004 1.302 0.027 1.298 0.009 NFKB1 1.236 0.050 NOX4 1.492 <.001 1.507 0.001 1.555 <.001 1.262 0.019 NPM1 1.287 0.036 NRIP3 1.219 0.031 1.218 0.018 NRP1 1.482 0.002 1.245 0.041 OLFML2B 1.362 0.015 OR51E1 1.531 <.001 1.488 0.003 PAK6 1.269 0.033 PATE1 1.308 <.001 1.332 <.001 1.164 0.044 PCNA 1.278 0.020 PEX10 1.436 0.005 1.393 0.009 PGD 1.298 0.048 1.579 <.001 PGK1 1.274 0.023 1.262 0.009 PLA2G7 1.315 0.011 1.346 0.005 PLAU 1.319 0.010 PLK1 1.309 0.021 1.563 <.001 1.410 0.002 1.372 0.003 PLOD2 1.284 0.019 1.272 0.014 1.332 0.005 POSTN 1.599 <.001 1.514 0.002 1.391 0.005 PPP3CA 1.402 0.007 1.316 0.018 PSMD13 1.278 0.040 1.297 0.033 1.279 0.017 1.373 0.004 PTK6 1.640 <.001 1.932 <.001 1.369 0.001 1.406 <.001 PTTG1 1.409 <.001 1.510 <.001 1.347 0.001 1.558 <.001 RAD21 1.315 0.035 1.402 0.004 1.589 <.001 1.439 <.001 RAF1 1.503 0.002 RALA 1.521 0.004 1.403 0.007 1.563 <.001 1.229 0.040 RALBP1 1.277 0.033 RGS7 1.154 0.015 1.266 0.010 RRM1 1.570 0.001 1.602 <.001 RRM2 1.368 <.001 1.289 0.004 1.396 <.001 1.230 0.015 SAT1 1.482 0.016 1.403 0.030 SDC1 1.340 0.018 1.396 0.018 SEC14L1 1.260 0.048 1.360 0.002 SESN3 1.485 <.001 1.631 <.001 1.232 0.047 1.292 0.014 SFRP4 1.800 <.001 1.814 <.001 1.496 <.001 1.289 0.027 SHMT2 1.807 <.001 1.658 <.001 1.673 <.001 1.548 <.001 SKIL 1.327 0.008 SLC25A21 1.398 0.001 1.285 0.018 SOX4 1.286 0.020 1.280 0.030 SPARC 1.539 <.001 1.842 <.001 1.269 0.026 SPP1 1.322 0.022 SQLE 1.359 0.020 1.270 0.036 STMN1 1.402 0.007 1.446 0.005 1.279 0.031 SULF1 1.587 <.001 TAF2 1.273 0.027 TFDP1 1.328 0.021 1.400 0.005 1.416 0.001 THBS2 1.812 <.001 1.960 <.001 1.320 0.012 1.256 0.038 THY1 1.362 0.020 1.662 <.001 TK1 1.251 0.011 1.377 <.001 1.401 <.001 TOP2A 1.670 <.001 1.920 <.001 1.869 <.001 1.927 <.001 TPD52 1.324 0.011 1.366 0.002 1.351 0.005 TPX2 1.884 <.001 2.154 <.001 1.874 <.001 1.794 <.001 UAP1 1.244 0.044 UBE2C 1.403 <.001 1.541 <.001 1.306 0.002 1.323 <.001 UBE2T 1.667 <.001 1.282 0.023 1.502 <.001 1.298 0.005 UGT2B15 1.295 0.001 1.275 0.002 UGT2B17 1.294 0.025 UHRF1 1.454 <.001 1.531 <.001 1.257 0.029 VCPIP1 1.390 0.009 1.414 0.004 1.294 0.021 1.283 0.021 WNT5A 1.274 0.038 1.298 0.020 XIAP 1.464 0.006 ZMYND8 1.277 0.048 ZWINT 1.259 0.047

TABLE 4B Genes significantly (p < 0.05) associated with cRFI or bRFI in the primary Gleason pattern or highest Gleason pattern with hazard ratio (HR) < 1.0 (increased expression is positively associated with good prognosis) cRFI cRFI bRFI bRFI Official Primary Pattern Highest Pattern Primary Pattern Highest Pattern Symbol HR p-value HR p-value HR p-value HR p-value AAMP 0.564 <.001 0.571 .001 0.764 0.037 0.786 0.034 ABCA5 0.755 <.001 0.695 <.001 0.800 0.006 ABCB1 0.777 0.026 ABCG2 0.788 0.033 0.784 0.040 0.803 0.018 0.750 0.004 ABHD2 0.734 0.011 ACE 0.782 0.048 ACOX2 0.639 <.001 0.631 <.001 0.713 <.001 0.716 0.002 ADH5 0.625 <.001 0.637 <.001 0.753 0.026 AKAP1 0.764 0.006 0.800 0.005 0.837 0.046 AKR1C1 0.773 0.033 0.802 0.032 AKT1 0.714 0.005 AKT3 0.811 0.015 0.809 0.021 ALDH1A2 0.606 <.001 0.498 <.001 0.613 <.001 0.624 <.001 AMPD3 0.793 0.024 ANPEP 0.584 <.001 0.493 <.001 ANXA2 0.753 0.013 0.781 0.036 0.762 0.008 0.795 0.032 APRT 0.758 0.026 0.780 0.044 0.746 0.008 ATXN1 0.673 0.001 0.776 0.029 0.809 0.031 0.812 0.043 AXIN2 0.674 <.001 0.571 <.001 0.776 0.005 0.757 0.005 AZGP1 0.585 <.001 0.652 <.001 0.664 <.001 0.746 <.001 BAD 0.765 0.023 BCL2 0.788 0.033 0.778 0.036 BDKRB1 0.728 0.039 BIK 0.712 0.005 BIN1 0.607 <.001 0.724 0.002 0.726 <.001 0.834 0.034 BTG3 0.847 0.034 BTRC 0.688 0.001 0.713 0.003 C7 0.589 <.001 0.639 <.001 0.629 <.001 0.691 <.001 CADM1 0.546 <.001 0.529 <.001 0.743 0.008 0.769 0.015 CASP1 0.769 0.014 0.799 0.028 0.799 0.010 0.815 0.018 CAV1 0.736 0.011 0.711 0.005 0.675 <.001 0.743 0.006 CAV2 0.636 0.010 0.648 0.012 0.685 0.012 CCL2 0.759 0.029 0.764 0.024 CCNH 0.689 <.001 0.700 <.001 CD164 0.664 <.001 0.651 <.001 CD1A 0.687 0.004 CD44 0.545 <.001 0.600 <.001 0.788 0.018 0.799 0.023 CD82 0.771 0.009 0.748 0.004 CDC25B 0.755 0.006 0.817 0.025 CDK14 0.845 0.043 CDK2 0.819 0.032 CDK3 0.733 0.005 0.772 0.006 0.838 0.017 CDKN1A 0.766 0.041 CDKN1C 0.662 <.001 0.712 0.002 0.693 <.001 0.761 0.009 CHN1 0.788 0.036 COL6A1 0.608 <.001 0.767 0.013 0.706 <.001 0.775 0.007 CSF1 0.626 <.001 0.709 0.003 CSK 0.837 0.029 C SRP1 0.793 0.024 0.782 0.019 C TNNB 1 0.898 0.042 0.885 <.001 CTSB 0.701 0.004 0.713 0.007 0.715 0.002 0.803 0.038 CTSK 0.815 0.042 CXCL12 0.652 <.001 0.802 0.044 0.711 0.001 CYP3A5 0.463 <.001 0.436 <.001 0.727 0.003 CYR61 0.652 0.002 0.676 0.002 DAP 0.761 0.026 0.775 0.025 0.802 0.048 DARC 0.725 0.005 0.792 0.032 DDR2 0.719 0.001 0.763 0.008 DES 0.619 <.001 0.737 0.005 0.638 <.001 0.793 0.017 DHRS9 0.642 0.003 DHX9 0.888 <.001 DLC1 0.710 0.007 0.715 0.009 DLGAP1 0.613 <.001 0.551 <.001 0.779 0.049 DNIVI3 0.679 <.001 0.812 0.037 DPP4 0.591 <.001 0.613 <.001 0.761 0.003 DPT 0.613 <.001 0.576 <.001 0.647 <.001 0.677 <.001 DUSP1 0.662 0.001 0.665 0.001 0.785 0.024 DUSP6 0.713 0.005 0.668 0.002 EDNRA 0.702 0.002 0.779 0.036 EGF 0.738 0.028 EGR1 0.569 <.001 0.577 <.001 0.782 0.022 EGR3 0.601 <.001 0.619 <.001 0.800 0.038 EIF253 0.756 0.015 EIF5 0.776 0.023 0.787 0.028 ELK4 0.628 <.001 0.658 <.001 EPHA2 0.720 0.011 0.663 0.004 EPHA3 0.727 0.003 0.772 0.005 ERBB2 0.786 0.019 0.738 0.003 0.815 0.041 ERBB3 0.728 0.002 0.711 0.002 0.828 0.043 0.813 0.023 ERCC1 0.771 0.023 0.725 0.007 0.806 0.049 0.704 0.002 EREG 0.754 0.016 0.777 0.034 ESR2 0.731 0.026 FAAH 0.708 0.004 0.758 0.012 0.784 0.031 0.774 0.007 FAM107A 0.517 <.001 0.576 <.001 0.642 <.001 0.656 <.001 FAM13C 0.568 <.001 0.526 <.001 0.739 0.002 0.639 <.001 FAS 0.755 0.014 FASLG 0.706 0.021 FGF10 0.653 <.001 0.685 <.001 0.766 0.022 FGF17 0.746 0.023 0.781 0.015 0.805 0.028 FGF7 0.794 0.030 0.820 0.037 0.811 0.040 FGFR2 0.683 <.001 0.686 <.001 0.674 <.001 0.703 <.001 FKBP5 0.676 0.001 FLNA 0.653 <.001 0.741 0.010 0.682 <.001 0.771 0.016 FLNC 0.751 0.029 0.779 0.047 0.663 <.001 0.725 <.001 FLT1 0.799 0.044 FOS 0.566 <.001 0.543 <.001 0.757 0.006 FOXO1 0.816 0.039 0.798 0.023 FOXQ1 0.753 0.017 0.757 0.024 0.804 0.018 FYN 0.779 0.031 GADD45B 0.590 <.001 0.619 <.001 GDF15 0.759 0.019 0.794 0.048 GHR 0.702 0.005 0.630 <.001 0.673 <.001 0.590 <.001 GNRH1 0.742 0.014 GPM6B 0.653 <.001 0.633 <.001 0.696 <.001 0.768 0.007 GSN 0.570 <.001 0.697 0.001 0.697 <.001 0.758 0.005 GSTM1 0.612 <.001 0.588 <.001 0.718 <.001 0.801 0.020 GSTM2 0.540 <.001 0.630 <.001 0.602 <.001 0.706 <.001 HGD 0.796 0.020 0.736 0.002 HIRIP3 0.753 0.011 0.824 0.050 HK1 0.684 <.001 0.683 <.001 0.799 0.011 0.804 0.014 HLA-G 0.726 0.022 HLF 0.555 <.001 0.582 <.001 0.703 <.001 0.702 <.001 HNF1B 0.690 <.001 0.585 <.001 HPS1 0.744 0.003 0.784 0.020 0.836 0.047 HSD3B2 0.733 0.016 HSP90AB1 0.801 0.036 HSPA5 0.776 0.034 HSPB1 0.813 0.020 HSPB2 0.762 0.037 0.699 0.002 0.783 0.034 HSPG2 0.794 0.044 ICAM1 0.743 0.024 0.768 0.040 IER3 0.686 0.002 0.663 <.001 IFIT1 0.649 <.001 0.761 0.026 IGF1 0.634 <.001 0.537 <.001 0.696 <.001 0.688 <.001 IGF2 0.732 0.004 IGFBP2 0.548 <.001 0.620 <.001 IGFBP5 0.681 <.001 IGFBP6 0.577 <.001 0.675 <.001 IL1B 0.712 0.005 0.742 0.009 IL6 0.763 0.028 IL6R 0.791 0.039 IL6ST 0.585 <.001 0.639 <.001 0.730 0.002 0.768 0.006 IL8 0.624 <.001 0.662 0.001 ILK 0.712 0.009 0.728 0.012 0.790 0.047 0.790 0.042 ING5 0.625 <.001 0.658 <.001 0.728 0.002 ITGA5 0.728 0.006 0.803 0.039 ITGA6 0.779 0.007 0.775 0.006 ITGA7 0.584 <.001 0.700 0.001 0.656 <.001 0.786 0.014 ITGAD 0.657 0.020 ITGB4 0.718 0.007 0.689 <.001 0.818 0.041 ITGB5 0.801 0.050 ITPR1 0.707 0.001 JUN 0.556 <.001 0.574 <.001 0.754 0.008 JUNB 0.730 0.017 0.715 0.010 KIT 0.644 0.004 0.705 0.019 0.605 <.001 0.659 0.001 KLC1 0.692 0.003 0.774 0.024 0.747 0.008 KLF6 0.770 0.032 0.776 0.039 KLK1 0.646 <.001 0.652 0.001 0.784 0.037 KLK10 0.716 0.006 KLK2 0.647 <.001 0.628 <.001 0.786 0.009 KLK3 0.706 <.001 0.748 <.001 0.845 0.018 KRT1 0.734 0.024 KRT15 0.627 <.001 0.526 <.001 0.704 <.001 0.782 0.029 KRT18 0.624 <.001 0.617 <.001 0.738 0.005 0.760 0.005 KRT5 0.640 <.001 0.550 <.001 0.740 <.001 0.798 0.023 KRT8 0.716 0.006 0.744 0.008 L1CAM 0.738 0.021 0.692 0.009 0.761 0.036 LAG3 0.741 0.013 0.729 0.011 LAMA4 0.686 0.011 0.592 0.003 LAMA5 0.786 0.025 LAMB3 0.661 <.001 0.617 <.001 0.734 <.001 LGALS3 0.618 <.001 0.702 0.001 0.734 0.001 0.793 0.012 LIG3 0.705 0.008 0.615 <.001 LRP1 0.786 0.050 0.795 0.023 0.770 0.009 MAP3K7 0.789 0.003 MGMT 0.632 <.001 0.693 <.001 MICA 0.781 0.014 0.653 <.001 0.833 0.043 MPPED2 0.655 <.001 0.597 <.001 0.719 <.001 0.759 0.006 MSH6 0.793 0.015 MTSS1 0.613 <.001 0.746 0.008 MVP 0.792 0.028 0.795 0.045 0.819 0.023 MYBPC1 0.648 <.001 0.496 <.001 0.701 <.001 0.629 <.001 NCAM1 0.773 0.015 NCAPD3 0.574 <.001 0.463 <.001 0.679 <.001 0.640 <.001 NEXN 0.701 0.002 0.791 0.035 0.725 0.002 0.781 0.016 NFAT5 0.515 <.001 0.586 <.001 0.785 0.017 NFATC2 0.753 0.023 NFKB IA 0.778 0.037 NRG1 0.644 0.004 0.696 0.017 0.698 0.012 OAZ1 0.777 0.034 0.775 0.022 OLFML3 0.621 <.001 0.720 0.001 0.600 <.001 0.626 <.001 OMD 0.706 0.003 OR51E2 0.820 0.037 0.798 0.027 PAGE4 0.549 <.001 0.613 <.001 0.542 <.001 0.628 <.001 PCA3 0.684 <.001 0.635 <.001 PCDHGB7 0.790 0.045 0.725 0.002 0.664 <.001 PGF 0.753 0.017 PGR 0.740 0.021 0.728 0.018 PIK3CG 0.803 0.024 PLAUR 0.778 0.035 PLG 0.728 0.028 PPAP2B 0.575 <.001 0.629 <.001 0.643 <.001 0.699 <.001 PPP1R12A 0.647 <.001 0.683 0.002 0.782 0.023 0.784 0.030 PRIMA1 0.626 <.001 0.658 <.001 0.703 0.002 0.724 0.003 PRKCA 0.642 <.001 0.799 0.029 0.677 0.001 0.776 0.006 PRKCB 0.675 0.001 0.648 <.001 0.747 0.006 PROM1 0.603 0.018 0.659 0.014 0.493 0.008 PTCH1 0.680 0.001 0.753 0.010 0.789 0.018 PTEN 0.732 0.002 0.747 0.005 0.744 <.001 0.765 0.002 PTGS2 0.596 <.001 0.610 <.001 PTH1R 0.767 0.042 0.775 0.028 0.788 0.047 PTHLH 0.617 0.002 0.726 0.025 0.668 0.002 0.718 0.007 PTK2B 0.744 0.003 0.679 <.001 0.766 0.002 0.726 <.001 PTPN1 0.760 0.020 0.780 0.042 PYCARD 0.748 0.012 RAB27A 0.708 0.004 RAB30 0.755 0.008 RAGE 0.817 0.048 RAP1B 0.818 0.050 RARB 0.757 0.007 0.677 <.001 0.789 0.007 0.746 0.003 RASSF1 0.816 0.035 RHOB 0.725 0.009 0.676 0.001 0.793 0.039 RLN1 0.742 0.033 0.762 0.040 RND3 0.636 <.001 0.647 <.001 RNF114 0.749 0.011 SDC2 0.721 0.004 SDHC 0.725 0.003 0.727 0.006 SEMA3A 0.757 0.024 0.721 0.010 SERPINA3 0.716 0.008 0.660 0.001 SERPINB5 0.747 0.031 0.616 0.002 SH3RF2 0.577 <.001 0.458 <.001 0.702 <.001 0.640 <.001 SLC22A3 0.565 <.001 0.540 <.001 0.747 0.004 0.756 0.007 SMAD4 0.546 <.001 0.573 <.001 0.636 <.001 0.627 <.001 SMARCD1 0.718 <.001 0.775 0.017 SMO 0.793 0.029 0.754 0.021 0.718 0.003 SOD1 0.757 0.049 0.707 0.006 SORBS1 0.645 <.001 0.716 0.003 0.693 <.001 0.784 0.025 SPARCL1 0.821 0.028 0.829 0.014 0.781 0.030 SPDEF 0.778 <.001 SPINT1 0.732 0.009 0.842 0.026 SRC 0.647 <.001 0.632 <.001 SRD5A1 0.813 0.040 SRD5A2 0.489 <.001 0.533 <.001 0.544 <.001 0.611 <.001 STS 0.713 0.002 0.783 0.011 0.725 <.001 0.827 0.025 STAT3 0.773 0.037 0.759 0.035 STAT5A 0.695 <.001 0.719 0.002 0.806 0.020 0.783 0.008 STAT5B 0.633 <.001 0.655 <.001 0.814 0.028 SUMO1 0.790 0.015 SVIL 0.659 <.001 0.713 0.002 0.711 0.002 0.779 0.010 TARP 0.800 0.040 TBP 0.761 0.010 TFF3 0.734 0.010 0.659 <.001 TGFB1I1 0.618 <.001 0.693 0.002 0.637 <.001 0.719 0.004 TGFB2 0.679 <.001 0.747 0.005 0.805 0.030 TGFB3 0.791 0.037 TGFBR2 0.778 0.035 TIMP3 0.751 0.011 TMPRSS2 0.745 0.003 0.708 <.001 TNF 0.670 0.013 0.697 0.015 TNFRSF10A 0.780 0.018 0.752 0.006 0.817 0.032 TNFRSF10B 0.576 <.001 0.655 <.001 0.766 0.004 0.778 0.002 TNFRSF18 0.648 0.016 0.759 0.034 TNFSF10 0.653 <.001 0.667 0.004 TP53 0.729 0.003 TP63 0.759 0.016 0.636 <.001 0.698 <.001 0.712 0.001 TPM1 0.778 0.048 0.743 0.012 0.783 0.032 0.811 0.046 TPM2 0.578 <.001 0.634 <.001 0.611 <.001 0.710 0.001 TPP2 0.775 0.037 TRAF3IP2 0.722 0.002 0.690 <.001 0.792 0.021 0.823 0.049 TRO 0.744 0.003 0.725 0.003 0.765 0.002 0.821 0.041 TUBB2A 0.639 <.001 0.625 <.001 TYMP 0.786 0.039 VCL 0.594 <.001 0.657 0.001 0.682 <.001 VEGFA 0.762 0.024 VEGFB 0.795 0.037 VIM 0.739 0.009 0.791 0.021 WDR19 0.776 0.015 WFDC1 0.746 <.001 YY1 0.683 0.001 0.728 0.002 ZFHX3 0.684 <.001 0.661 <.001 0.801 0.010 0.762 0.001 ZFP36 0.605 <.001 0.579 <.001 0.815 0.043 ZNF827 0.624 <.001 0.730 0.007 0.738 0.004

Tables 5A and 5B provide genes that were significantly associated (p<0.05), positively or negatively, with recurrence (cRFI, bRFI) after adjusting for AUA risk group in the primary and/or highest Gleason pattern. Increased expression of genes in Table 5A is negatively associated with good prognosis, while increased expression of genes in Table 5B is positively associated with good prognosis.

TABLE 5A Genes significantly (p < 0.05) associated with cRFI or bRFI after adjustment for AIA risk grous in primary Gleason pattern or highest Gleason pattern with hazard ratio (HR) > 1.0 (increased expression is positively associated with good prognosis) cRFI cRFI bRFI bRFI Official Primary Pattern Highest Pattern Primary Pattern Highest Pattern Symbol HR p-value HR p-value HR p-value HR p-value AKR1C3 1.315 0.018 1.283 0.024 ALOX12 1.198 0.024 ANLN 1.406 <.001 1.519 <.001 1.485 <.001 1.632 <.001 AQP2 1.209 <.001 1.302 <.001 ASAP2 1.582 <.001 1.333 0.011 1.307 0.019 ASPN 1.872 <.001 1.741 <.001 1.638 <.001 1.691 <.001 ATP5E 1.309 0.042 1.369 0.012 BAG5 1.291 0.044 BAX 1.298 0.025 1.420 0.004 BGN 1.746 <.001 1.755 <.001 BIRC5 1.480 <.001 1.470 <.001 1.419 <.001 1.503 <.001 BMP6 1.536 <.001 1.815 <.001 1.294 0.033 1.429 0.001 BRCA2 1.184 0.037 BUB1 1.288 0.001 1.391 <.001 1.254 <.001 1.189 0.018 CACNA1D 1.313 0.029 CADPS 1.358 0.007 1.267 0.022 CASP3 1.251 0.037 CCNB1 1.261 0.033 1.318 0.005 CCNE2 1.345 0.005 1.438 <.001 1.606 <.001 1.426 <.001 CD276 1.482 0.002 1.668 <.001 1.451 <.001 1.302 0.011 CDC20 1.417 <.001 1.547 <.001 1.355 <.001 1.446 <.001 CDC6 1.340 0.011 1.265 0.046 1.367 0.002 1.272 0.025 CDH7 1.402 0.003 1.409 0.002 CDKN2B 1.553 <.001 1.746 <.001 1.340 0.014 1.369 0.006 CDKN2C 1.411 <.001 1.604 <.001 1.220 0.033 CDKN3 1.296 0.004 1.226 0.015 CENPF 1.434 0.002 1.570 <.001 1.633 <.001 1.610 <.001 CKS2 1.419 0.008 1.374 0.022 1.380 0.004 COL1A1 1.677 <.001 1.809 <.001 1.401 <.001 1.352 0.003 COL1A2 1.373 0.010 COL3A1 1.669 <.001 1.781 <.001 1.249 0.024 1.234 0.047 COL4A1 1.475 0.002 1.513 0.002 COL8A1 1.506 0.001 1.691 <.001 CRISP3 1.406 0.004 1.471 <.001 CTHRC1 1.426 0.009 1.793 <.001 1.311 0.019 CTNND2 1.462 <.001 DDIT4 1.478 0.003 1.783 <.001 1.236 0.039 DYNLL1 1.431 0.002 1.193 0.004 EIF3H 1.372 0.027 ENY2 1.325 0.023 1.270 0.017 ERG 1.303 0.041 EZH2 1.254 0.049 F2R 1.540 0.002 1.448 0.006 1.286 0.023 FADD 1.235 0.041 1.404 <.001 FAP 1.386 0.015 1.440 0.008 1.253 0.048 FASN 1.303 0.028 FCGR3A 1.439 0.011 1.262 0.045 FGF5 1.289 0.006 GNPTAB 1.290 0.033 1.369 0.022 1.285 0.018 1.355 0.008 GPR68 1.396 0.005 GREM1 1.341 0.022 1.502 0.003 1.366 0.006 HDAC1 1.329 0.016 HDAC9 1.378 0.012 HRAS 1.465 0.006 HSD17B4 1.442 <.001 1.245 0.028 IGFBP3 1.366 0.019 1.302 0.011 INHBA 2.000 <.001 2.336 <.001 1.486 0.002 JAG1 1.251 0.039 KCNN2 1.347 0.020 1.524 <.001 1.312 0.023 1.346 0.011 KHDRBS3 1.500 0.001 1.426 0.001 1.267 0.032 KIAA0196 1.272 0.028 KIF4A 1.199 0.022 1.262 0.004 KPNA2 1.252 0.016 LAMA3 1.332 0.004 1.356 0.010 LAMB1 1.317 0.028 LAMC1 1.516 0.003 1.302 0.040 1.397 0.007 LIMS1 1.261 0.027 LOX 1.265 0.016 1.372 0.001 LTBP2 1.477 0.002 LUM 1.321 0.020 MANF 1.647 <.001 1.284 0.027 MCM2 1.372 0.003 1.302 0.032 MCM3 1.269 0.047 MCM6 1.276 0.033 1.245 0.037 MELK 1.294 0.005 1.394 <.001 MK167 1.253 0.028 1.246 0.029 MMP11 1.557 <.001 1.290 0.035 1.357 0.005 MRPL13 1.275 0.003 MSH2 1.355 0.009 MYBL2 1.497 <.001 1.509 <.001 1.304 0.003 1.292 0.007 MY06 1.367 0.010 NDRG1 1.270 0.042 1.314 0.025 NEK2 1.338 0.020 1.269 0.026 NETO2 1.434 0.004 1.303 0.033 1.283 0.012 NOX4 1.413 0.006 1.308 0.037 1.444 <.001 NRIP3 1.171 0.026 NRP1 1.372 0.020 ODC1 1.450 <.001 OR51E1 1.559 <.001 1.413 0.008 PAK6 1.233 0.047 PATE1 1.262 <.001 1.375 <.001 1.143 0.034 1.191 0.036 PCNA 1.227 0.033 1.318 0.003 PEX10 1.517 <.001 1.500 0.001 PGD 1.363 0.028 1.316 0.039 1.652 <.001 PGK1 1.224 0.034 1.206 0.024 PIM1 1.205 0.042 PLA2G7 1.298 0.018 1.358 0.005 PLAU 1.242 0.032 PLK1 1.464 0.001 1.299 0.018 1.275 0.031 PLOD2 1.206 0.039 1.261 0.025 POSTN 1.558 0.001 1.356 0.022 1.363 0.009 PPP3CA 1.445 0.002 PSMD13 1.301 0.017 1.411 0.003 PTK2 1.318 0.031 PTK6 1.582 <.001 1.894 <.001 1.290 0.011 1.354 0.003 PTTG1 1.319 0.004 1.430 <.001 1.271 0.006 1.492 <.001 RAD21 1.278 0.028 1.435 0.004 1.326 0.008 RAF1 1.504 <.001 RALA 1.374 0.028 1.459 0.001 RGS7 1.203 0.031 RRM1 1.535 0.001 1.525 <.001 RRM2 1.302 0.003 1.197 0.047 1.342 <.001 SAT1 1.374 0.043 SDC1 1.344 0.011 1.473 0.008 SEC14L1 1.297 0.006 SESN3 1.337 0.002 1.495 <.001 1.223 0.038 SFRP4 1.610 <.001 1.542 0.002 1.370 0.009 SHMT2 1.567 0.001 1.522 <.001 1.485 0.001 1.370 <.001 SKIL 1.303 0.008 SLC25A21 1.287 0.020 1.306 0.017 SLC44A1 1.308 0.045 SNRPB2 1.304 0.018 SOX4 1.252 0.031 SPARC 1.445 0.004 1.706 <.001 1.269 0.026 SPP1 1.376 0.016 SQLE 1.417 0.007 1.262 0.035 STAT1 1.209 0.029 STMN1 1.315 0.029 SULF1 1.504 0.001 TAF2 1.252 0.048 1.301 0.019 TFDP1 1.395 0.010 1.424 0.002 THBS2 1.716 <.001 1.719 <.001 THY1 1.343 0.035 1.575 0.001 TK1 1.320 <.001 1.304 <.001 TOP2A 1.464 0.001 1.688 <.001 1.715 <.001 1.761 <.001 TPD52 1.286 0.006 1.258 0.023 TPX2 1.644 <.001 1.964 <.001 1.699 <.001 1.754 <.001 TYMS 1.315 0.014 UBE2C 1.270 0.019 1.558 <.001 1.205 0.027 1.333 <.001 UBE2G1 1.302 0.041 UBE2T 1.451 <.001 1.309 0.003 UGT2B15 1.222 0.025 UHRF1 1.370 0.003 1.520 <.001 1.247 0.020 VCPIP1 1.332 0.015 VTI1B 1.237 0.036 XIAP 1.486 0.008 ZMYND8 1.408 0.007 ZNF3 1.284 0.018 ZWINT 1.289 0.028

TABLE 5B Genes significantly (p < 0.05) associated with cRFI or bRFI after adjustment for AUA risk group in the primary Gleason pattern or highest Gleason pattern with hazard ratio (HR) < 1.0 (increased expression is positively associated with good prognosis) Table 5B cRFI cRFI bRFI bRFI Official Primary Pattern Highest Pattern Primary Pattern Highest Pattern Symbol HR p-value HR p-value HR p-value HR p-value AAMP 0.535 <.001 0.581 <.001 0.700 0.002 0.759 0.006 ABCA5 0.798 0.007 0.745 0.002 0.841 0.037 ABCC1 0.800 0.044 ABCC4 0.787 0.022 ABHD2 0.768 0.023 ACOX2 0.678 0.002 0.749 0.027 0.759 0.004 ADH5 0.645 <.001 0.672 0.001 AGTR1 0.780 0.030 AKAP1 0.815 0.045 0.758 <.001 AKT1 0.732 0.010 ALDH1A2 0.646 <.001 0.548 <.001 0.671 <.001 0.713 0.001 ANPEP 0.641 <.001 0.535 <.001 ANXA2 0.772 0.035 0.804 0.046 ATXN1 0.654 <.001 0.754 0.020 0.797 0.017 AURKA 0.788 0.030 AXIN2 0.744 0.005 0.655 <.001 AZGP1 0.656 <.001 0.676 <.001 0.754 0.001 0.791 0.004 BAD 0.700 0.004 BIN1 0.650 <.001 0.764 0.013 0.803 0.015 BTG3 0.836 0.025 BTRC 0.730 0.005 C7 0.617 <.001 0.680 <.001 0.667 <.001 0.755 0.005 CADM1 0.559 <.001 0.566 <.001 0.772 0.020 0.802 0.046 CASP1 0.781 0.030 0.779 0.021 0.818 0.027 0.828 0.036 CAV1 0.775 0.034 CAV2 0.677 0.019 CCL2 0.752 0.023 CCNH 0.679 <.001 0.682 <.001 CD164 0.721 0.002 0.724 0.005 CD1A 0.710 0.014 CD44 0.591 <.001 0.642 <.001 CD82 0.779 0.021 0.771 0.024 CDC25B 0.778 0.035 0.818 0.023 CDK14 0.788 0.011 CDK3 0.752 0.012 0.779 0.005 0.841 0.020 CDKN1A 0.770 0.049 0.712 0.014 CDKN1C 0.684 <.001 0.697 <.001 CHN1 0.772 0.031 COL6A1 0.648 <.001 0.807 0.046 0.768 0.004 CSF1 0.621 <.001 0.671 0.001 CTNNB1 0.905 0.008 CTSB 0.754 0.030 0.716 0.011 0.756 0.014 CXCL12 0.641 <.001 0.796 0.038 0.708 <.001 CYP3A5 0.503 <.001 0.528 <.001 0.791 0.028 CYR61 0.639 0.001 0.659 0.001 0.797 0.048 DARC 0.707 0.004 DDR2 0.750 0.011 DES 0.657 <.001 0.758 0.022 0.699 <.001 DHRS9 0.625 0.002 DHX9 0.846 <.001 DIAPH1 0.682 0.007 0.723 0.008 0.780 0.026 DLC1 0.703 0.005 0.702 0.008 DLGAP1 0.703 0.008 0.636 <.001 DNM3 0.701 0.001 0.817 0.042 DPP4 0.686 <.001 0.716 0.001 DPT 0.636 <.001 0.633 <.001 0.709 0.006 0.773 0.024 DUSP1 0.683 0.006 0.679 0.003 DUSP6 0.694 0.003 0.605 <.001 EDN1 0.773 0.031 EDNRA 0.716 0.007 EGR1 0.575 <.001 0.575 <.001 0.771 0.014 EGR3 0.633 0.002 0.643 <.001 0.792 0.025 EIF4E 0.722 0.002 ELK4 0.710 0.009 0.759 0.027 ENPP2 0.786 0.039 EPHA2 0.593 0.001 EPHA3 0.739 0.006 0.802 0.020 ERBB2 0.753 0.007 ERBB3 0.753 0.009 0.753 0.015 ERCC1 0.727 0.001 EREG 0.722 0.012 0.769 0.040 ESR1 0.742 0.015 FABP5 0.756 0.032 FAM107A 0.524 <.001 0.579 <.001 0.688 <.001 0.699 0.001 FAM13C 0.639 <.001 0.601 <.001 0.810 0.019 0.709 <.001 FAS 0.770 0.033 FASLG 0.716 0.028 0.683 0.017 FGF10 0.798 0.045 FGF17 0.718 0.018 0.793 0.024 0.790 0.024 FGFR2 0.739 0.007 0.783 0.038 0.740 0.004 FGFR4 0.746 0.050 FKBP5 0.689 0.003 FLNA 0.701 0.006 0.766 0.029 0.768 0.037 FLNC 0.755 <.001 0.820 0.022 FLT1 0.729 0.008 FOS 0.572 <.001 0.536 <.001 0.750 0.005 FOXQ1 0.778 0.033 0.820 0.018 FYN 0.708 0.006 GADD45B 0.577 <.001 0.589 <.001 GDF15 0.757 0.013 0.743 0.006 GHR 0.712 0.004 0.679 0.001 GNRH1 0.791 0.048 GPM6B 0.675 <.001 0.660 <.001 0.735 <.001 0.823 0.049 GSK3B 0.783 0.042 GSN 0.587 <.001 0.705 0.002 0.745 0.004 0.796 0.021 GSTM1 0.686 0.001 0.631 <.001 0.807 0.018 GSTM2 0.607 <.001 0.683 <.001 0.679 <.001 0.800 0.027 HIRIP3 0.692 <.001 0.782 0.007 HK1 0.724 0.002 0.718 0.002 HLF 0.580 <.001 0.571 <.001 0.759 0.008 0.750 0.004 HNF1B 0.669 <.001 HPS1 0.764 0.008 HSD17B10 0.802 0.045 HSD17B2 0.723 0.048 HSD3B2 0.709 0.010 HSP90AB1 0.780 0.034 0.809 0.041 HSPA5 0.738 0.017 HSPB1 0.770 0.006 0.801 0.032 HSPB2 0.788 0.035 ICAM1 0.728 0.015 0.716 0.010 IER3 0.735 0.016 0.637 <.001 0.802 0.035 IFIT1 0.647 <.001 0.755 0.029 IGF1 0.675 <.001 0.603 <.001 0.762 0.006 0.770 0.030 IGF2 0.761 0.011 IGFBP2 0.601 <.001 0.605 <.001 IGFBP5 0.702 <.001 IGFBP6 0.628 <.001 0.726 0.003 IL1B 0.676 0.002 0.716 0.004 IL6 0.688 0.005 0.766 0.044 IL6R 0.786 0.036 IL6ST 0.618 <.001 0.639 <.001 0.785 0.027 0.813 0.042 IL8 0.635 <.001 0.628 <.001 ILK 0.734 0.018 0.753 0.026 ING5 0.684 <.001 0.681 <.001 0.756 0.006 ITGA4 0.778 0.040 ITGA5 0.762 0.026 ITGA6 0.811 0.038 ITGA7 0.592 <.001 0.715 0.006 0.710 0.002 ITGAD 0.576 0.006 ITGB4 0.693 0.003 ITPR1 0.789 0.029 JUN 0.572 <.001 0.581 <.001 0.777 0.019 JUNB 0.732 0.030 0.707 0.016 KCTD12 0.758 0.036 KIT 0.691 0.009 0.738 0.028 KLC1 0.741 0.024 0.781 0.024 KLF6 0.733 0.018 0.727 0.014 KLK1 0.744 0.028 KLK2 0.697 0.002 0.679 <.001 KLK3 0.725 <.001 0.715 <.001 0.841 0.023 KRT15 0.660 <.001 0.577 <.001 0.750 0.002 KRT18 0.623 <.001 0.642 <.001 0.702 <.001 0.760 0.006 KRT2 0.740 0.044 KRT5 0.674 <.001 0.588 <.001 0.769 0.005 KRT8 0.768 0.034 L1CAM 0.737 0.036 LAG3 0.711 0.013 0.748 0.029 LAMA4 0.649 0.009 LAMB3 0.709 0.002 0.684 0.006 0.768 0.006 LGALS3 0.652 <.001 0.752 0.015 0.805 0.028 LIG3 0.728 0.016 0.667 <.001 LRP1 0.811 0.043 MDM2 0.788 0.033 MGMT 0.645 <.001 0.766 0.015 MICA 0.796 0.043 0.676 <.001 NIPPED2 0.675 <.001 0.616 <.001 0.750 0.006 MRC1 0.788 0.028 MTSS1 0.654 <.001 0.793 0.036 MYBPC1 0.706 <.001 0.534 <.001 0.773 0.004 0.692 <.001 NCAPD3 0.658 <.001 0.566 <.001 0.753 0.011 0.733 0.009 NCOR1 0.838 0.045 NEXN 0.748 0.025 0.785 0.020 NFAT5 0.531 <.001 0.626 <.001 NFATC2 0.759 0.024 OAZ1 0.766 0.024 OLFML3 0.648 <.001 0.748 0.005 0.639 <.001 0.675 <.001 OR51E2 0.823 0.034 PAGE4 0.599 <.001 0.698 0.002 0.606 <.001 0.726 <.001 PCA3 0.705 <.001 0.647 <.001 PCDHGB7 0.712 <.001 PGF 0.790 0.039 PLG 0.764 0.048 PLP2 0.766 0.037 PPAP2B 0.589 <.001 0.647 <.001 0.691 <.001 0.765 0.013 PPP1R12A 0.673 0.001 0.677 0.001 0.807 0.045 PRIMA1 0.622 <.001 0.712 0.008 0.740 0.013 PRKCA 0.637 <.001 0.694 <.001 PRKCB 0.741 0.020 0.664 <.001 PROM1 0.599 0.017 0.527 0.042 0.610 0.006 0.420 0.002 PTCH1 0.752 0.027 0.762 0.011 PTEN 0.779 0.011 0.802 0.030 0.788 0.009 PTGS2 0.639 <.001 0.606 <.001 PTHLH 0.632 0.007 0.739 0.043 0.654 0.002 0.740 0.015 PTK2B 0.775 0.019 0.831 0.028 0.810 0.017 PTPN1 0.721 0.012 0.737 0.024 PYCARD 0.702 0.005 RAB27A 0.736 0.008 RAB30 0.761 0.011 RARB 0.746 0.010 RASSF1 0.805 0.043 RHOB 0.755 0.029 0.672 0.001 RLN1 0.742 0.036 0.740 0.036 RND3 0.607 <.001 0.633 <.001 RNF114 0.782 0.041 0.747 0.013 SDC2 0.714 0.002 SDHC 0.698 <.001 0.762 0.029 SERPINA3 0.752 0.030 SERPINB5 0.669 0.014 SH3RF2 0.705 0.012 0.568 <.001 0.755 0.016 SLC22A3 0.650 <.001 0.582 <.001 SMAD4 0.636 <.001 0.684 0.002 0.741 0.007 0.738 0.007 SMARCD1 0.757 0.001 SMO 0.790 0.049 0.766 0.013 SOD1 0.741 0.037 0.713 0.007 SORBS1 0.684 0.003 0.732 0.008 0.788 0.049 SPDEF 0.840 0.012 SPINT1 0.837 0.048 SRC 0.674 <.001 0.671 <.001 SRD5A2 0.553 <.001 0.588 <.001 0.618 <.001 0.701 <.001 ST5 0.747 0.012 0.761 0.010 0.780 0.016 0.832 0.041 STAT3 0.735 0.020 STAT5A 0.731 0.005 0.743 0.009 0.817 0.027 STAT5B 0.708 <.001 0.696 0.001 SUMO1 0.815 0.037 SVIL 0.689 0.003 0.739 0.008 0.761 0.011 TBP 0.792 0.037 TFF3 0.719 0.007 0.664 0.001 TGFB1I1 0.676 0.003 0.707 0.007 0.709 0.005 0.777 0.035 TGFB2 0.741 0.010 0.785 0.017 TGFBR2 0.759 0.022 TIMP3 0.785 0.037 TMPRSS2 0.780 0.012 0.742 <.001 TNF 0.654 0.007 0.682 0.006 TNFRSF10B 0.623 <.001 0.681 <.001 0.801 0.018 0.815 0.019 TNFSF10 0.721 0.004 TP53 0.759 0.011 TP63 0.737 0.020 0.754 0.007 TPM2 0.609 <.001 0.671 <.001 0.673 <.001 0.789 0.031 TRAF3IP2 0.795 0.041 0.727 0.005 TRO 0.793 0.033 0.768 0.027 0.814 0.023 TUBB2A 0.626 <.001 0.590 <.001 VCL 0.613 <.001 0.701 0.011 VIM 0.716 0.005 0.792 0.025 WFDC1 0.824 0.029 YY1 0.668 <.001 0.787 0.014 0.716 0.001 0.819 0.011 ZFHX3 0.732 <.001 0.709 <.001 ZFP36 0.656 0.001 0.609 <.001 0.818 0.045 ZNF827 0.750 0.022

Tables 6A and 6B provide genes that were significantly associated (p<0.05), positively or negatively, with recurrence (cRFI, bRFI) after adjusting for Gleason pattern in the primary and/or highest Gleason pattern. Increased expression of genes in Table 6A is negatively associated with good prognosis, while increased expression of gene in Table 6B is positively associated with good prognosis.

TABLE 6A Genes significantly (p < 0.05) associated with cRFI or bRFI after adjustment for Gleason pattern in the primary Gleason pattern or highest Gleason pattern with a hazard ratio (HR) >1.0 (increased expression is negatively associated with good prognosis) Table 6A cRFI cRFI bRFI bRFI Official Primary Pattern Highest Pattern Primary Pattern Highest Pattern Symbol HR p-value HR p-value HR p-value HR p-value AKR1C3 1.258 0.039 ANLN 1.292 0.023 1.449 <.001 1.420 0.001 AQP2 1.178 0.008 1.287 <.001 ASAP2 1.396 0.015 ASPN 1.809 <.001 1.508 0.009 1.506 0.002 1.438 0.002 BAG5 1.367 0.012 BAX 1.234 0.044 BGN 1.465 0.009 1.342 0.046 BIRC5 1.338 0.008 1.364 0.004 1.279 0.006 BMP6 1.369 0.015 1.518 0.002 BUB1 1.239 0.024 1.227 0.001 1.236 0.004 CACNA1D 1.337 0.025 CADPS 1.280 0.029 CCNE2 1.256 0.043 1.577 <.001 1.324 0.001 CD276 1.320 0.029 1.396 0.007 1.279 0.033 CDC20 1.298 0.016 1.334 0.002 1.257 0.032 1.279 0.003 CDH7 1.258 0.047 1.338 0.013 CDKN2B 1.342 0.032 1.488 0.009 CDKN2C 1.344 0.010 1.450 <.001 CDKN3 1.284 0.012 CENPF 1.289 0.048 1.498 0.001 1.344 0.010 COL1A1 1.481 0.003 1.506 0.002 COL3A1 1.459 0.004 1.430 0.013 COL4A1 1.396 0.015 COL8A1 1.413 0.008 CRISP3 1.346 0.012 1.310 0.025 CTHRC1 1.588 0.002 DDIT4 1.363 0.020 1.379 0.028 DICER1 1.294 0.008 ENY2 1.269 0.024 FADD 1.307 0.010 FAS 1.243 0.025 FGF5 1.328 0.002 GNPTAB 1.246 0.037 GREM1 1.332 0.024 1.377 0.013 1.373 0.011 HDAC1 1.301 0.018 1.237 0.021 HSD17B4 1.277 0.011 IFN-γ 1.219 0.048 IMMT 1.230 0.049 INHBA 1.866 <.001 1.944 <.001 JAG1 1.298 0.030 KCNN2 1.378 0.020 1.282 0.017 KHDRBS3 1.353 0.029 1.305 0.014 LAMA3 1.344 <.001 1.232 0.048 LAMC1 1.396 0.015 LIMS1 1.337 0.004 LOX 1.355 0.001 1.341 0.002 LTBP2 1.304 0.045 MAGEA4 1.215 0.024 MANF 1.460 <.001 MCM6 1.287 0.042 1.214 0.046 MELK 1.329 0.002 MMP11 1.281 0.050 MRPL13 1.266 0.021 MYBL2 1.453 <.001 1.274 0.019 MYC 1.265 0.037 MY06 1.278 0.047 NET02 1.322 0.022 NFKB1 1.255 0.032 NOX4 1.266 0.041 OR51E1 1.566 <.001 1.428 0.003 PATE1 1.242 <.001 1.347 <.001 1.177 0.011 PCNA 1.251 0.025 PEX10 1.302 0.028 PGD 1.335 0.045 1.379 0.014 1.274 0.025 PIM1 1.254 0.019 PLA2G7 1.289 0.025 1.250 0.031 PLAU 1.267 0.031 PSMD13 1.333 0.005 PTK6 1.432 <.001 1.577 <.001 1.223 0.040 PTTG1 1.279 0.013 1.308 0.006 RAGE 1.329 0.011 RALA 1.363 0.044 1.471 0.003 RGS7 1.120 0.040 1.173 0.031 RRM1 1.490 0.004 1.527 <.001 SESN3 1.353 0.017 SFRP4 1.370 0.025 SHMT2 1.460 0.008 1.410 0.006 1.407 0.008 1.345 <.001 SKIL 1.307 0.025 SLC25A21 1.414 0.002 1.330 0.004 SMARCC2 1.219 0.049 SPARC 1.431 0.005 TFDP1 1.283 0.046 1.345 0.003 THBS2 1.456 0.005 1.431 0.012 TK1 1.214 0.015 1.222 0.006 TOP2A 1.367 0.018 1.518 0.001 1.480 <.001 TPX2 1.513 0.001 1.607 <.001 1.588 <.001 1.481 <.001 UBE2T 1.409 0.002 1.285 0.018 UGT2B15 1.216 0.009 1.182 0.021 XIAP 1.336 0.037 1.194 0.043

TABLE 6B Genes significantly (p < 0.05) associated with cRFI or bRFI after adjustment for Gleason pattern in the primary Gleason pattern or highest Gleason pattern with hazard ration (HR) < 1.0 (increased expression is positively associated with good prognosis) Table 6B cRFI cRFI bRFI bRFI Official Primary Pattern Highest Pattern Primary Pattern Highest Pattern Symbol HR p-value HR p-value HR p-value HR p-value AAMP 0.660 0.001 0.675 <.001 0.836 0.045 ABCA5 0.807 0.014 0.737 <.001 0.845 0.030 ABCC1 0.780 0.038 0.794 0.015 ABCG2 0.807 0.035 ABHD2 0.720 0.002 ADH5 0.750 0.034 AKAP1 0.721 <.001 ALDH1A2 0.735 0.009 0.592 <.001 0.756 0.007 0.781 0.021 ANGPT2 0.741 0.036 ANPEP 0.637 <.001 0.536 <.001 ANXA2 0.762 0.044 APOE 0.707 0.013 APRT 0.727 0.004 0.771 0.006 ATXN1 0.725 0.013 AURKA 0.784 0.037 0.735 0.003 AXIN2 0.744 0.004 0.630 <.001 AZGP1 0.672 <.001 0.720 <.001 0.764 0.001 BAD 0.687 <.001 BAK1 0.783 0.014 BCL2 0.777 0.033 0.772 0.036 BIK 0.768 0.040 BIN1 0.691 <.001 BTRC 0.776 0.029 C7 0.707 0.004 0.791 0.024 CADM1 0.587 <.001 0.593 <.001 CASP1 0.773 0.023 0.820 0.025 CAV1 0.753 0.014 CAV2 0.627 0.009 0.682 0.003 CCL2 0.740 0.019 CCNH 0.736 0.003 CCR1 0.755 0.022 CD1A 0.740 0.025 CD44 0.590 <.001 0.637 <.001 CD68 0.757 0.026 CD82 0.778 0.012 0.759 0.016 CDC25B 0.760 0.021 CDK3 0.762 0.024 0.774 0.007 CDKN1A 0.714 0.015 CDKN1C 0.738 0.014 0.768 0.021 COL6A1 0.690 <.001 0.805 0.048 CSF1 0.675 0.002 0.779 0.036 CSK 0.825 0.004 CTNNB1 0.884 0.045 0.888 0.027 CTSB 0.740 0.017 0.676 0.003 0.755 0.010 CTSD 0.673 0.031 0.722 0.009 CTSK 0.804 0.034 CTSL2 0.748 0.019 CXCL12 0.731 0.017 CYP3A5 0.523 <.001 0.518 <.001 CYR61 0.744 0.041 DAP 0.755 0.011 DARC 0.763 0.029 DDR2 0.813 0.041 DES 0.743 0.020 DHRS9 0.606 0.001 DHX9 0.916 0.021 DIAPH1 0.749 0.036 0.688 0.003 DLGAP1 0.758 0.042 0.676 0.002 DLL4 0.779 0.010 DNIVI3 0.732 0.007 DPP4 0.732 0.004 0.750 0.014 DPT 0.704 0.014 DUSP6 0.662 <.001 0.665 0.001 EBNA1BP2 0.828 0.019 EDNRA 0.782 0.048 EGF 0.712 0.023 EGR1 0.678 0.004 0.725 0.028 EGR3 0.680 0.006 0.738 0.027 EIF2C2 0.789 0.032 EIF253 0.759 0.012 ELK4 0.745 0.024 EPHA2 0.661 0.007 EPHA3 0.781 0.026 0.828 0.037 ERBB2 0.791 0.022 0.760 0.014 0.789 0.006 ERBB3 0.757 0.009 ERCC1 0.760 0.008 ESR1 0.742 0.014 ESR2 0.711 0.038 ETV4 0.714 0.035 FAM107A 0.619 <.001 0.710 0.011 0.781 0.019 FAM13C 0.664 <.001 0.686 <.001 0.813 0.014 F AM49B 0.670 <.001 0.793 0.014 0.815 0.044 0.843 0.047 FASLG 0.616 0.004 0.813 0.038 FGF10 0.751 0.028 0.766 0.019 FGF17 0.718 0.031 0.765 0.019 FGFR2 0.740 0.009 0.738 0.002 FKBP5 0.749 0.031 FLNC 0.826 0.029 FLT1 0.779 0.045 0.729 0.006 FLT4 0.815 0.024 FOS 0.657 0.003 0.656 0.004 FSD1 0.763 0.017 FYN 0.716 0.004 0.792 0.024 GADD45B 0.692 0.009 0.697 0.010 GDF15 0.767 0.016 GHR 0.701 0.002 0.704 0.002 0.640 <.001 GNRH1 0.778 0.039 GPM6B 0.749 0.010 0.750 0.010 0.827 0.037 GRB7 0.696 0.005 GSK3B 0.726 0.005 GSN 0.660 <.001 0.752 0.019 GSTM1 0.710 0.004 0.676 <.001 GSTM2 0.643 <.001 0.767 0.015 HK1 0.798 0.035 HLA-G 0.660 0.013 HLF 0.644 <.001 0.727 0.011 HNF1B 0.755 0.013 HPS1 0.756 0.006 0.791 0.043 HSD17B10 0.737 0.006 HSD3B2 0.674 0.003 HSP90AB1 0.763 0.015 HSPB1 0.787 0.020 0.778 0.015 HSPE1 0.794 0.039 ICAM1 0.664 0.003 IER3 0.699 0.003 0.693 0.010 IFIT1 0.621 <.001 0.733 0.027 IGF1 0.751 0.017 0.655 <.001 IGFBP2 0.599 <.001 0.605 <.001 IGFBP5 0.745 0.007 0.775 0.035 IGFBP6 0.671 0.005 IL1B 0.732 0.016 0.717 0.005 IL6 0.763 0.040 IL6R 0.764 0.022 IL6ST 0.647 <.001 0.739 0.012 IL8 0.711 0.015 0.694 0.006 ING5 0.729 0.007 0.727 0.003 ITGA4 0.755 0.009 ITGA5 0.743 0.018 0.770 0.034 ITGA6 0.816 0.044 0.772 0.006 ITGA7 0.680 0.004 ITGAD 0.590 0.009 ITGB4 0.663 <.001 0.658 <.001 0.759 0.004 JUN 0.656 0.004 0.639 0.003 KIAA0196 0.737 0.011 KIT 0.730 0.021 0.724 0.008 KLC1 0.755 0.035 KLK1 0.706 0.008 KLK2 0.740 0.016 0.723 0.001 KLK3 0.765 0.006 0.740 0.002 KRT1 0.774 0.042 KRT15 0.658 <.001 0.632 <.001 0.764 0.008 KRT18 0.703 0.004 0.672 <.001 0.779 0.015 0.811 0.032 KRT5 0.686 <.001 0.629 <.001 0.802 0.023 KRT8 0.763 0.034 0.771 0.022 L1CAM 0.748 0.041 LAG3 0.693 0.008 0.724 0.020 LAMA4 0.689 0.039 LAMB3 0.667 <.001 0.645 <.001 0.773 0.006 LGALS3 0.666 <.001 0.822 0.047 LIG3 0.723 0.008 LRP1 0.777 0.041 0.769 0.007 MDM2 0.688 <.001 MET 0.709 0.010 0.736 0.028 0.715 0.003 MGMT 0.751 0.031 MICA 0.705 0.002 MPPED2 0.690 0.001 0.657 <.001 0.708 <.001 MRC1 0.812 0.049 MSH6 0.860 0.049 MTSS1 0.686 0.001 MVP 0.798 0.034 0.761 0.033 MYBPC1 0.754 0.009 0.615 <.001 NCAPD3 0.739 0.021 0.664 0.005 NEXN 0.798 0.037 NFAT5 0.596 <.001 0.732 0.005 NFATC2 0.743 0.016 0.792 0.047 NOS3 0.730 0.012 0.757 0.032 OAZ1 0.732 0.020 0.705 0.002 OCLN 0.746 0.043 0.784 0.025 OLFML3 0.711 0.002 0.709 <.001 0.720 0.001 OMD 0.729 0.011 0.762 0.033 OSM 0.813 0.028 PAGE4 0.668 0.003 0.725 0.004 0.688 <.001 0.766 0.005 PCA3 0.736 0.001 0.691 <.001 PCDHGB7 0.769 0.019 0.789 0.022 PIK3CA 0.768 0.010 PIK3CG 0.792 0.019 0.758 0.009 PLG 0.682 0.009 PPAP2B 0.688 0.005 0.815 0.046 PPP1R12A 0.731 0.026 0.775 0.042 PRIMA1 0.697 0.004 0.757 0.032 PRKCA 0.743 0.019 PRKCB 0.756 0.036 0.767 0.029 PROM1 0.640 0.027 0.699 0.034 0.503 0.013 PTCH1 0.730 0.018 PTEN 0.779 0.015 0.789 0.007 PTGS2 0.644 <.001 0.703 0.007 PTHLH 0.655 0.012 0.706 0.038 0.634 0.001 0.665 0.003 PTK2B 0.779 0.023 0.702 0.002 0.806 0.015 0.806 0.024 PYCARD 0.659 0.001 RAB30 0.779 0.033 0.754 0.014 RARB 0.787 0.043 0.742 0.009 RAS SF1 0.754 0.005 RHOA 0.796 0.041 0.819 0.048 RND3 0.721 0.011 0.743 0.028 SDC1 0.707 0.011 SDC2 0.745 0.002 SDHC 0.750 0.013 SERPINA3 0.730 0.016 SERPINB5 0.715 0.041 SH3RF2 0.698 0.025 SIPA1L1 0.796 0.014 0.820 0.004 SLC22A3 0.724 0.014 0.700 0.008 SMAD4 0.668 0.002 0.771 0.016 SMARCD1 0.726 <.001 0.700 0.001 0.812 0.028 SMO 0.785 0.027 SOD1 0.735 0.012 SORBS1 0.785 0.039 SPDEF 0.818 0.002 SPINT1 0.761 0.024 0.773 0.006 SRC 0.709 <.001 0.690 <.001 SRD5A1 0.746 0.010 0.767 0.024 0.745 0.003 SRD5A2 0.575 <.001 0.669 0.001 0.674 <.001 0.781 0.018 ST5 0.774 0.027 STAT1 0.694 0.004 STAT5A 0.719 0.004 0.765 0.006 0.834 0.049 STAT5B 0.704 0.001 0.744 0.012 SUMO1 0.777 0.014 SVIL 0.771 0.026 TBP 0.774 0.031 TFF3 0.742 0.015 0.719 0.024 TGFB1I1 0.763 0.048 TGFB2 0.729 0.011 0.758 0.002 TMPRSS2 0.810 0.034 0.692 <.001 TNF 0.727 0.022 TNFRSF10A 0.805 0.025 TNFRSF10B 0.581 <.001 0.738 0.014 0.809 0.034 TNFSF10 0.751 0.015 0.700 <.001 TP63 0.723 0.018 0.736 0.003 TPM2 0.708 0.010 0.734 0.014 TRAF3IP2 0.718 0.004 TRO 0.742 0.012 TSTA3 0.774 0.028 TUBB2A 0.659 <.001 0.650 <.001 TYMP 0.695 0.002 VCL 0.683 0.008 VIM 0.778 0.040 WDR19 0.775 0.014 XRC C 5 0.793 0.042 YY1 0.751 0.025 0.810 0.008 ZFHX3 0.760 0.005 0.726 0.001 ZFP36 0.707 0.008 0.672 0.003 ZNF827 0.667 0.002 0.792 0.039

Tables 7A and 7B provide genes significantly associated (p<0.05), positively or negatively, with clinical recurrence (cRFI) in negative TMPRSS fusion specimens in the primary or highest Gleason pattern specimen. Increased expression of genes in Table 7A is negatively associated with good prognosis, while increased expression of genes in Table 7B is positively associated with good prognosis.

TABLE 7A Genes significantly (p < 0.05) associated with cRFI for TMPRSS2-ERG fusion negative in the primary Gleason pattern or highest Gleason pattern with hazard ratio (HR) > 1.0 (increased expression is negatively associated with good prognosis) Primary Pattern Highest Pattern Official Symbol HR p-value HR p-value ANLN 1.42 0.012 1.36 0.004 AQP2 1.25 0.033 ASPN 2.48 <.001 1.65 <.001 BGN 2.04 <.001 1.45 0.007 BIRC5 1.59 <.001 1.37 0.005 BMP6 1.95 <.001 1.43 0.012 BMPR1B 1.93 0.002 BUB1 1.51 <.001 1.35 <.001 CCNE2 1.48 0.007 CD276 1.93 <.001 1.79 <.001 CDC20 1.49 0.004 1.47 <.001 CDC6 1.52 0.009 1.34 0.022 CDKN2B 1.54 0.008 1.55 0.003 CDKN2C 1.55 0.003 1.57 <.001 CDKN3 1.34 0.026 CENPF 1.63 0.002 1.33 0.018 CKS2 1.50 0.026 1.43 0.009 CLTC 1.46 0.014 COL1A1 1.98 <.001 1.50 0.002 COL3A1 2.03 <.001 1.42 0.007 COL4A1 1.81 0.002 COL8A1 1.63 0.004 1.60 0.001 CRISP3 1.31 0.016 CTHRC1 1.67 0.006 1.48 0.005 DDIT4 1.49 0.037 ENY2 1.29 0.039 EZH2 1.35 0.016 F2R 1.46 0.034 1.46 0.007 FAP 1.66 0.006 1.38 0.012 FGF5 1.46 0.001 GNPTAB 1.49 0.013 HSD17B4 1.34 0.039 1.44 0.002 INHBA 2.92 <.001 2.19 <.001 JAG1 1.38 0.042 KCNN2 1.71 0.002 1.73 <.001 KHDRBS3 1.46 0.015 KLK14 1.28 0.034 KPNA2 1.63 0.016 LAMC1 1.41 0.044 LOX 1.29 0.036 LTBP2 1.57 0.017 MELK 1.38 0.029 MMP11 1.69 0.002 1.42 0.004 MYBL2 1.78 <.001 1.49 <.001 NETO2 2.01 <.001 1.43 0.007 NME1 1.38 0.017 PATE1 1.43 <.001 1.24 0.005 PEX10 1.46 0.030 PGD 1.77 0.002 POSTN 1.49 0.037 1.34 0.026 PPFIA3 1.51 0.012 PPP3CA 1.46 0.033 1.34 0.020 PTK6 1.69 <.001 1.56 <.001 PTTG1 1.35 0.028 RAD51 1.32 0.048 RALBP1 1.29 0.042 RGS7 1.18 0.012 1.32 0.009 RRM1 1.57 0.016 1.32 0.041 RRM2 1.30 0.039 SAT1 1.61 0.007 SESN3 1.76 <.001 1.36 0.020 SFRP4 1.55 0.016 1.48 0.002 SHMT2 2.23 <.001 1.59 <.001 SPARC 1.54 0.014 SQLE 1.86 0.003 STMN1 2.14 <.001 THBS2 1.79 <.001 1.43 0.009 TK1 1.30 0.026 TOP2A 2.03 <.001 1.47 0.003 TPD52 1.63 0.003 TPX2 2.11 <.001 1.63 <.001 TRAP1 1.46 0.023 UBE2C 1.57 <.001 1.58 <.001 UBE2G1 1.56 0.008 UBE2T 1.75 <.001 UGT2B15 1.31 0.036 1.33 0.004 UHRF1 1.46 0.007 UTP23 1.52 0.017

TABLE 7B Genes significantly (p < 0.05) associated with cRFI for TMPRSS2-ERG fusion negative in the primary Gleason pattern or highest Gleason pattern with hazard ratio (HR) < 1.0 (increased expression is positively associated with good prognosis) Primary Pattern Highest Pattern Official Symbol HR p-value HR p-value AAMP 0.56 <.001 0.65 0.001 ABCA5 0.64 <.001 0.71 <.001 ABCB1 0.62 0.004 ABCC3 0.74 0.031 ABCG2 0.78 0.050 ABHD2 0.71 0.035 ACOX2 0.54 <.001 0.71 0.007 ADH5 0.49 <.001 0.61 <.001 AKAP1 0.77 0.031 0.76 0.013 AKR1C1 0.65 0.006 0.78 0.044 AKT1 0.72 0.020 AKT3 0.75 <.001 ALDH1A2 0.53 <.001 0.60 <.001 AMPD3 0.62 <.001 0.78 0.028 ANPEP 0.54 <.001 0.61 <.001 ANXA2 0.63 0.008 0.74 0.016 ARHGAP29 0.67 0.005 0.77 0.016 ARHGDIB 0.64 0.013 ATP5J 0.57 0.050 ATXN1 0.61 0.004 0.77 0.043 AXIN2 0.51 <.001 0.62 <.001 AZGP1 0.61 <.001 0.64 <.001 BCL2 0.64 0.004 0.75 0.029 BIN1 0.52 <.001 0.74 0.010 BTG3 0.75 0.032 0.75 0.010 BTRC 0.69 0.011 C7 0.51 <.001 0.67 <.001 CADM1 0.49 <.001 0.76 0.034 CASP1 0.71 0.010 0.74 0.007 CAV1 0.73 0.015 CCL5 0.67 0.018 0.67 0.003 CCNH 0.63 <.001 0.75 0.004 CCR1 0.77 0.032 CD164 0.52 <.001 0.63 <.001 CD44 0.53 <.001 0.74 0.014 CDH10 0.69 0.040 CDH18 0.40 0.011 CDK14 0.75 0.013 CDK2 0.81 0.031 CDK3 0.73 0.022 CDKN1A 0.68 0.038 CDKN1C 0.62 0.003 0.72 0.005 COL6A1 0.54 <.001 0.70 0.004 COL6A3 0.64 0.004 CSF1 0.56 <.001 0.78 0.047 CSRP1 0.40 <.001 0.66 0.002 CTGF 0.66 0.015 0.74 0.027 CTNNB1 0.69 0.043 CTSB 0.60 0.002 0.71 0.011 CTSS 0.67 0.013 CXCL12 0.56 <.001 0.77 0.026 CYP3A5 0.43 <.001 0.63 <.001 CYR61 0.43 <.001 0.58 <.001 DAG1 0.72 0.012 DARC 0.66 0.016 DDR2 0.65 0.007 DES 0.52 <.001 0.74 0.018 DHRS9 0.54 0.007 DICER1 0.70 0.044 DLC1 0.75 0.021 DLGAP1 0.55 <.001 0.72 0.005 DNIVI3 0.61 0.001 DPP4 0.55 <.001 0.77 0.024 DPT 0.48 <.001 0.61 <.001 DUSP1 0.47 <.001 0.59 <.001 DUSP6 0.65 0.009 0.65 0.002 DYNLL1 0.74 0.045 EDNRA 0.61 0.002 0.75 0.038 EFNB2 0.71 0.043 EGR1 0.43 <.001 0.58 <.001 EGR3 0.47 <.001 0.66 <.001 EIF5 0.77 0.028 ELK4 0.49 <.001 0.72 0.012 EPHA2 0.70 0.007 EPHA3 0.62 <.001 0.72 0.009 EPHB2 0.68 0.009 ERBB2 0.64 <.001 0.63 <.001 ERBB3 0.69 0.018 ERCC1 0.69 0.019 0.77 0.021 ESR2 0.61 0.020 FAAH 0.57 <.001 0.77 0.035 FABP5 0.67 0.035 FAM107A 0.42 <.001 0.59 <.001 FAM13C 0.53 <.001 0.59 <.001 FAS 0.71 0.035 FASLG 0.56 0.017 0.67 0.014 FGF10 0.57 0.002 FGF17 0.70 0.039 0.70 0.010 FGF7 0.63 0.005 0.70 0.004 FGFR2 0.63 0.003 0.71 0.003 FKBP5 0.72 0.020 FLNA 0.48 <.001 0.74 0.022 FOS 0.45 <.001 0.56 <.001 FOXO1 0.59 <.001 FOXQ1 0.57 <.001 0.69 0.008 FYN 0.62 0.001 0.74 0.013 G6PD 0.77 0.014 GADD45A 0.73 0.045 GADD45B 0.45 <.001 0.64 0.001 GDF15 0.58 <.001 GHR 0.62 0.008 0.68 0.002 GPM6B 0.60 <.001 0.70 0.003 GSK3B 0.71 0.016 0.71 0.006 GSN 0.46 <.001 0.66 <.001 GSTM1 0.56 <.001 0.62 <.001 GSTM2 0.47 <.001 0.67 <.001 HGD 0.72 0.002 HIRIP3 0.69 0.021 0.69 0.002 HK1 0.68 0.005 0.73 0.005 HLA-G 0.54 0.024 0.65 0.013 HLF 0.41 <.001 0.68 0.001 HNF1B 0.55 <.001 0.59 <.001 HPS1 0.74 0.015 0.76 0.025 HSD17B3 0.65 0.031 HSPB2 0.62 0.004 0.76 0.027 ICAM1 0.61 0.010 IER3 0.55 <.001 0.67 0.003 IFIT1 0.57 <.001 0.70 0.008 IFNG 0.69 0.040 IGF1 0.63 <.001 0.59 <.001 IGF2 0.67 0.019 0.70 0.005 IGFBP2 0.53 <.001 0.63 <.001 IGFBP5 0.57 <.001 0.71 0.006 IGFBP6 0.41 <.001 0.71 0.012 IL10 0.59 0.020 IL1B 0.53 <.001 0.70 0.005 IL6 0.55 0.001 IL6ST 0.45 <.001 0.68 <.001 IL8 0.60 0.005 0.70 0.008 ILK 0.68 0.029 0.76 0.036 ING5 0.54 <.001 0.82 0.033 ITGA1 0.66 0.017 ITGA3 0.70 0.020 ITGA5 0.64 0.011 ITGA6 0.66 0.003 0.74 0.006 ITGA7 0.50 <.001 0.71 0.010 ITGB4 0.63 0.014 0.73 0.010 ITPR1 0.55 <.001 ITPR3 0.76 0.007 JUN 0.37 <.001 0.54 <.001 JUNB 0.58 0.002 0.71 0.016 KCTD12 0.68 0.017 KIT 0.49 0.002 0.76 0.043 KLC1 0.61 0.005 0.77 0.045 KLF 6 0.65 0.009 KLK1 0.68 0.036 KLK10 0.76 0.037 KLK2 0.64 <.001 0.73 0.006 KLK3 0.65 <.001 0.76 0.021 KLRK1 0.63 0.005 KRT15 0.52 <.001 0.58 <.001 KRT18 0.46 <.001 KRT5 0.51 <.001 0.58 <.001 KRT8 0.53 <.001 L1CAM 0.65 0.031 LAG3 0.58 0.002 0.76 0.033 LAMA4 0.52 0.018 LAMB3 0.60 0.002 0.65 0.003 LGALS3 0.52 <.001 0.71 0.002 LIG3 0.65 0.011 LRP1 0.61 0.001 0.75 0.040 MGMT 0.66 0.003 MICA 0.59 0.001 0.68 0.001 MLXIP 0.70 0.020 MMP2 0.68 0.022 MMP9 0.67 0.036 MPPED2 0.57 <.001 0.66 <.001 MRC1 0.69 0.028 MTSS1 0.63 0.005 0.79 0.037 MVP 0.62 <.001 MYBPC1 0.53 <.001 0.70 0.011 NCAM1 0.70 0.039 0.77 0.042 NCAPD3 0.52 <.001 0.59 <.001 NDRG1 0.69 0.008 NEXN 0.62 0.002 NFAT5 0.45 <.001 0.59 <.001 NFATC2 0.68 0.035 0.75 0.036 NFKBIA 0.70 0.030 NRG1 0.59 0.022 0.71 0.018 OAZ1 0.69 0.018 0.62 <.001 OLFML3 0.59 <.001 0.72 0.003 OR51E2 0.73 0.013 PAGE4 0.42 <.001 0.62 <.001 PCA3 0.53 <.001 PCDHGB7 0.70 0.032 PGF 0.68 0.027 0.71 0.013 PGR 0.76 0.041 PIK3C2A 0.80 <.001 PIK3CA 0.61 <.001 0.80 0.036 PIK3CG 0.67 0.001 0.76 0.018 PLP2 0.65 0.015 0.72 0.010 PPAP2B 0.45 <.001 0.69 0.003 PPP1R12A 0.61 0.007 0.73 0.017 PRIMA1 0.51 <.001 0.68 0.004 PRKCA 0.55 <.001 0.74 0.009 PRKCB 0.55 <.001 PROM1 0.67 0.042 PROS1 0.73 0.036 PTCH1 0.69 0.024 0.72 0.010 PTEN 0.54 <.001 0.64 <.001 PTGS2 0.48 <.001 0.55 <.001 PTH1R 0.57 0.003 0.77 0.050 PTHLH 0.55 0.010 PTK2B 0.56 <.001 0.70 0.001 PYCARD 0.73 0.009 RAB27A 0.65 0.009 0.71 0.014 RAB30 0.59 0.003 0.72 0.010 RAGE 0.76 0.011 RARB 0.59 <.001 0.63 <.001 RASSF1 0.67 0.003 RB1 0.67 0.006 RFX1 0.71 0.040 0.70 0.003 RHOA 0.71 0.038 0.65 <.001 RHOB 0.58 0.001 0.71 0.006 RND3 0.54 <.001 0.69 0.003 RNF114 0.59 0.004 0.68 0.003 SCUBE2 0.77 0.046 SDHC 0.72 0.028 0.76 0.025 SEC23A 0.75 0.029 SEMA3A 0.61 0.004 0.72 0.011 SEPT9 0.66 0.013 0.76 0.036 SERPINB5 0.75 0.039 SH3RF2 0.44 <.001 0.48 <.001 SHH 0.74 0.049 SLC22A3 0.42 <.001 0.61 <.001 SMAD4 0.45 <.001 0.66 <.001 SMARCD1 0.69 0.016 SOD1 0.68 0.042 SORBS1 0.51 <.001 0.73 0.012 SPARCL1 0.58 <.001 0.77 0.040 SPDEF 0.77 <.001 SPINT1 0.65 0.004 0.79 0.038 SRC 0.61 <.001 0.69 0.001 SRD5A2 0.39 <.001 0.55 <.001 STS 0.61 <.001 0.73 0.012 STAT1 0.64 0.006 STAT3 0.63 0.010 STAT5A 0.62 0.001 0.70 0.003 STAT5B 0.58 <.001 0.73 0.009 SUMO1 0.66 <.001 SVIL 0.57 0.001 0.74 0.022 TBP 0.65 0.002 TFF1 0.65 0.021 TFF3 0.58 <.001 TGFB1I1 0.51 <.001 0.75 0.026 TGFB2 0.48 <.001 0.62 <.001 TGFBR2 0.61 0.003 TIAM1 0.68 0.019 TIMP2 0.69 0.020 TIMP3 0.58 0.002 TNFRSF10A 0.73 0.047 TNFRSF10B 0.47 <.001 0.70 0.003 TNFSF10 0.56 0.001 TP63 0.67 0.001 TPM1 0.58 0.004 0.73 0.017 TPM2 0.46 <.001 0.70 0.005 TRA2A 0.68 0.013 TRAF3IP2 0.73 0.041 0.71 0.004 TRO 0.72 0.016 0.71 0.004 TUBB2A 0.53 <.001 0.73 0.021 TYMP 0.70 0.011 VCAM1 0.69 0.041 VCL 0.46 <.001 VEGFA 0.77 0.039 VEGFB 0.71 0.035 VIM 0.60 0.001 XRCC5 0.75 0.026 YY1 0.62 0.008 0.77 0.039 ZFHX3 0.53 <.001 0.58 <.001 ZFP36 0.43 <.001 0.54 <.001 ZNF827 0.55 0.001

Tables 8A and 8B provide genes that were significantly associated (p<0.05), positively or negatively, with clinical recurrence (cRFI) in positive TMPRSS fusion specimens in the primary or highest Gleason pattern specimen. Increased expression of genes in Table 8A is negatively associated with good prognosis, while increased expression of genes in Table 8B is positively associated with good prognosis.

TABLE 8A Genes significantly (p < 0.05) associated with cRFI for TMPRSS2-ERG fusion positive in the primary Gleason pattern or highest Gleason pattern with hazard ratio (HR) > 1.0 (increased expression is negatively associated with good prognosis) Primary Pattern Highest Pattern Official Symbol HR p-value HR p-value ACTR2 1.78 0.017 AKR1C3 1.44 0.013 ALCAM 1.44 0.022 ANLN 1.37 0.046 1.81 <.001 APOE 1.49 0.023 1.66 0.005 AQP2 1.30 0.013 ARHGMB 1.55 0.021 ASPN 2.13 <.001 2.43 <.001 ATP5E 1.69 0.013 1.58 0.014 BGN 1.92 <.001 2.55 <.001 BIRC5 1.48 0.006 1.89 <.001 BMP6 1.51 0.010 1.96 <.001 BRCA2 1.41 0.007 BUB1 1.36 0.007 1.52 <.001 CCNE2 1.55 0.004 1.59 <.001 CD276 1.65 <.001 CDC20 1.68 <.001 1.74 <.001 CDH11 1.50 0.017 CDH18 1.36 <.001 CDH7 1.54 0.009 1.46 0.026 CDKN2B 1.68 0.008 1.93 0.001 CDKN2C 2.01 <.001 1.77 <.001 CDKN3 1.51 0.002 1.33 0.049 CENPF 1.51 0.007 2.04 <.001 CKS2 1.43 0.034 1.56 0.007 COL1A1 2.23 <.001 3.04 <.001 COL1A2 1.79 0.001 2.22 <.001 COL3A1 1.96 <.001 2.81 <.001 COL4A1 1.52 0.020 COL5A1 1.50 0.020 COL5A2 1.64 0.017 1.55 0.010 COL8A1 1.96 <.001 2.38 <.001 CRISP3 1.68 0.002 1.67 0.002 CTHRC1 2.06 <.001 CTNND2 1.42 0.046 1.50 0.025 CTSK 1.43 0.049 CXCR4 1.82 0.001 1.64 0.007 DDIT4 1.54 0.016 1.58 0.009 DLL4 1.51 0.007 DYNLL1 1.50 0.021 1.22 0.002 F2R 2.27 <.001 2.02 <.001 FAP 2.12 <.001 FCGR3A 1.94 0.002 FGF5 1.23 0.047 FOXP3 1.52 0.006 1.48 0.018 GNPTAB 1.44 0.042 GPR68 1.51 0.011 GREM1 1.91 <.001 2.38 <.001 HDAC1 1.43 0.048 HDAC9 1.65 <.001 1.67 0.004 HRAS 1.65 0.005 1.58 0.021 IGFBP3 1.94 <.001 1.85 <.001 INHBA 2.03 <.001 2.64 <.001 JAG1 1.41 0.027 1.50 0.008 KCTD12 1.51 0.017 KHDRBS3 1.48 0.029 1.54 0.014 KPNA2 1.46 0.050 LAMA3 1.35 0.040 LAMC1 1.77 0.012 LTBP2 1.82 <.001 LUM 1.51 0.021 1.53 0.009 MELK 1.38 0.020 1.49 0.001 MKI67 1.37 0.014 MMP11 1.73 <.001 1.69 <.001 MRPL13 1.30 0.046 MYBL2 1.56 <.001 1.72 <.001 MYLK3 1.17 0.007 NOX4 1.58 0.005 1.96 <.001 NRIP3 1.30 0.040 NRP1 1.53 0.021 OLFML2B 1.54 0.024 OSM 1.43 0.018 PATE1 1.20 <.001 1.33 <.001 PCNA 1.64 0.003 PEX10 1.41 0.041 1.64 0.003 PIK3CA 1.38 0.037 PLK1 1.52 0.009 1.67 0.002 PLOD2 1.65 0.002 POSTN 1.79 <.001 2.06 <.001 PTK6 1.67 0.002 2.38 <.001 PTTG1 1.56 0.002 1.54 0.003 RAD21 1.61 0.036 1.53 0.005 RAD51 1.33 0.009 RALA 1.95 0.004 1.60 0.007 REG4 1.43 0.042 ROBO2 1.46 0.024 RRM1 1.44 0.033 RRM2 1.50 0.003 1.48 <.001 SAT1 1.42 0.009 1.43 0.012 SEC14L1 1.64 0.002 SFRP4 2.07 <.001 2.40 <.001 SHMT2 1.52 0.030 1.60 0.001 SLC44A1 1.42 0.039 SPARC 1.93 <.001 2.21 <.001 SULF1 1.63 0.006 2.04 <.001 THBS2 1.95 <.001 2.26 <.001 THY1 1.69 0.016 1.95 0.002 TK1 1.43 0.003 TOP2A 1.57 0.002 2.11 <.001 TPX2 1.84 <.001 2.27 <.001 UBE2C 1.41 0.011 1.44 0.006 UBE2T 1.63 0.001 UHRF1 1.51 0.007 1.69 <.001 WISP1 1.47 0.045 WNT5A 1.35 0.027 1.63 0.001 ZWINT 1.36 0.045

TABLE 8B Genes significantly (p < 0.05) associated with cRFI for TMPRSS2-ERG fusion positive in the primary Gleason pattern or highest Gleason pattern with hazard ratio (HR) < 1.0 (increased expression is positively associated with good prognosis) Primary Pattern Highest Pattern Official Symbol HR p-value HR p-value AAMP 0.57 0.007 0.58 <.001 ABCA5 0.80 0.044 ACE 0.65 0.023 0.55 <.001 ACOX2 0.55 <.001 ADH5 0.68 0.022 AKAP1 0.81 0.043 ALDH1A2 0.72 0.036 0.43 <.001 ANPEP 0.66 0.022 0.46 <.001 APRT 0.73 0.040 AXIN2 0.60 <.001 AZGP1 0.57 <.001 0.65 <.001 BCL2 0.69 0.035 BIK 0.71 0.045 BIN1 0.71 0.004 0.71 0.009 BTRC 0.66 0.003 0.58 <.001 C7 0.64 0.006 CADM1 0.61 <.001 0.47 <.001 CCL2 0.73 0.042 CCNH 0.69 0.022 CD44 0.56 <.001 0.58 <.001 CD82 0.72 0.033 CDC25B 0.74 0.028 CDH1 0.75 0.030 0.72 0.010 CDH19 0.56 0.015 CDK3 0.78 0.045 CDKN1C 0.74 0.045 0.70 0.014 CSF1 0.72 0.037 CTSB 0.69 0.048 CTSL2 0.58 0.005 CYP3A5 0.51 <.001 0.30 <.001 DHX9 0.89 0.006 0.87 0.012 DLC1 0.64 0.023 DLGAP1 0.69 0.010 0.49 <.001 DPP4 0.64 <.001 0.56 <.001 DPT 0.63 0.003 EGR1 0.69 0.035 EGR3 0.68 0.025 EIF2S3 0.70 0.021 EIF5 0.71 0.030 ELK4 0.71 0.041 0.60 0.003 EPHA2 0.72 0.036 0.66 0.011 EPHB 4 0.65 0.007 ERCC1 0.68 0.023 ESR2 0.64 0.027 FAM107A 0.64 0.003 0.61 0.003 FAM13C 0.68 0.006 0.55 <.001 FGFR2 0.73 0.033 0.59 <.001 FKBP5 0.60 0.006 FLNC 0.68 0.024 0.65 0.012 FLT1 0.71 0.027 FOS 0.62 0.006 FOXO1 0.75 0.010 GADD45B 0.68 0.020 GHR 0.62 0.006 GPM6B 0.57 <.001 GSTM1 0.68 0.015 0.58 <.001 GSTM2 0.65 0.005 0.47 <.001 HGD 0.63 0.001 0.71 0.020 HK1 0.67 0.003 0.62 0.002 HLF 0.59 <.001 HNF1B 0.66 0.004 0.61 0.001 IER3 0.70 0.026 IGF1 0.63 0.005 0.55 <.001 IGF1R 0.76 0.049 IGFBP2 0.59 0.007 0.64 0.003 IL6ST 0.65 0.005 IL8 0.61 0.005 0.66 0.019 ILK 0.64 0.015 ING5 0.73 0.033 0.70 0.009 ITGA7 0.72 0.045 0.69 0.019 ITGB4 0.63 0.002 KLC1 0.74 0.045 KLK1 0.56 0.002 0.49 <.001 KLK10 0.68 0.013 KLK11 0.66 0.003 KLK2 0.66 0.045 0.65 0.011 KLK3 0.75 0.048 0.77 0.014 KRT15 0.71 0.017 0.50 <.001 KRT5 0.73 0.031 0.54 <.001 LAMAS 0.70 0.044 LAMB3 0.70 0.005 0.58 <.001 LGALS3 0.69 0.025 LIG3 0.68 0.022 MDK 0.69 0.035 MGMT 0.59 0.017 0.60 <.001 MGST1 0.73 0.042 MICA 0.70 0.009 MPPED2 0.72 0.031 0.54 <.001 MTSS1 0.62 0.003 MYBPC1 0.50 <.001 NCAPD3 0.62 0.007 0.38 <.001 NCOR1 0.82 0.048 NFAT5 0.60 0.001 0.62 <.001 NRG1 0.66 0.040 0.61 0.029 NUP62 0.75 0.037 OMD 0.54 <.001 PAGE4 0.64 0.005 PCA3 0.66 0.012 PCDHGB7 0.68 0.018 PGR 0.60 0.012 PPAP2B 0.62 0.010 PPP1R12A 0.73 0.031 0.58 0.003 PRIMA1 0.65 0.013 PROM1 0.41 0.013 PTCH1 0.64 0.006 PTEN 0.75 0.047 PTGS2 0.67 0.011 PTK2B 0.66 0.005 PTPN1 0.71 0.026 RAGE 0.70 0.012 RARB 0.68 0.016 RGS10 0.84 0.034 RHOB 0.66 0.016 RND3 0.63 0.004 SDHC 0.73 0.044 0.69 0.016 SERPINA3 0.67 0.011 0.51 <.001 SERPINB5 0.42 <.001 SH3RF2 0.66 0.012 0.51 <.001 SLC22A3 0.59 0.003 0.48 <.001 SMAD4 0.64 0.004 0.49 <.001 SMARCC2 0.73 0.042 SMARCD1 0.73 <.001 0.76 0.035 SMO 0.64 0.006 SNAI1 0.53 0.008 SOD1 0.60 0.003 SRC 0.64 <.001 0.61 <.001 SRD5A2 0.63 0.004 0.59 <.001 STAT3 0.64 0.014 STAT5A 0.70 0.032 STAT5B 0.74 0.034 0.63 0.003 SVIL 0.71 0.028 TGFB1I1 0.68 0.036 TMPRSS2 0.72 0.015 0.67 <.001 TNFRSF10A 0.69 0.010 TNFRSF10B 0.67 0.007 0.64 0.001 TNFRSF18 0.38 0.003 TNFSF10 0.71 0.025 TP53 0.68 0.004 0.57 <.001 TP63 0.75 0.049 0.52 <.001 TPM2 0.62 0.007 TRAF3IP2 0.71 0.017 0.68 0.005 TRO 0.72 0.033 TUBB2A 0.69 0.038 VCL 0.62 <.001 VEGFA 0.71 0.037 WWOX 0.65 0.004 ZFHX3 0.77 0.011 0.73 0.012 ZFP36 0.69 0.018 ZNF827 0.68 0.013 0.49 <.001

Tables 9A and 9B provide genes significantly associated (p<0.05), positively or negatively, with TMPRSS fusion status in the primary Gleason pattern. Increased expression of genes in Table 9A are positively associated with TMPRSS fusion positivity, while increased expression of genes in Table 10A are negatively associated with TMPRSS fusion positivity.

TABLE 9A Genes significantly (p < 0.05) associated with TMPRSS fusion status in the primary Gleason pattern with odds ratio (OR) > 1.0 (increased expression is positively associated with TMPRSS fusion positivity Official Symbol p-value Odds Ratio ABCC8 <.001 1.86 ALDH18A1 0.005 1.49 ALKBH3 0.043 1.30 ALOX5 <.001 1.66 AMPD3 <.001 3.92 APEX1 <.001 2.00 ARHGD113 <.001 1.87 ASAP2 0.019 1.48 ATXN1 0.013 1.41 BMPR1B <.001 2.37 CACNA1D <.001 9.01 CADPS 0.015 1.39 CD276 0.003 2.25 CDH1 0.016 1.37 CDH7 <.001 2.22 CDK7 0.025 1.43 COL9A2 <.001 2.58 CRISP3 <.001 2.60 CTNND1 0.033 1.48 ECE1 <.001 2.22 EIF5 0.023 1.34 EPHB4 0.005 1.51 ERG <.001 14.5 FAM171B 0.047 1.32 FAM73A 0.008 1.45 FASN 0.004 1.50 GNPTAB <.001 1.60 GPS1 0.006 1.45 GRB7 0.023 1.38 HDAC1 <.001 4.95 HGD <.001 1.64 HIP1 <.001 1.90 HNF1B <.001 3.55 HSPA8 0.041 1.32 IGF1R 0.001 1.73 ILF3 <.001 1.91 IMMT 0.025 1.36 ITPR1 <.001 2.72 ITPR3 <.001 5.91 JAG1 0.007 1.42 KCNN2 <.001 2.80 KHDRBS3 <.001 2.63 KIAA0247 0.019 1.38 KLK11 <.001 1.98 LAMC1 0.008 1.56 LAMC2 <.001 3.30 LOX 0.009 1.41 LRP1 0.044 1.30 MAP3K5 <.001 2.06 MAP7 <.001 2.74 MSH2 0.005 1.59 MSH3 0.006 1.45 MUC1 0.012 1.42 MYO6 <.001 3.79 NCOR2 0.001 1.62 NDRG1 <.001 6.77 NETO2 <.001 2.63 ODC1 <.001 1.98 OR51E1 <.001 2.24 PDE9A <.001 2.21 PEX10 <.001 3.41 PGK1 0.022 1.33 PLA2G7 <.001 5.51 PPP3CA 0.047 1.38 PSCA 0.013 1.43 PSMD13 0.004 1.51 PTCH1 0.022 1.38 PTK2 0.014 1.38 PTK6 <.001 2.29 PTK7 <.001 2.45 PTPRK <.001 1.80 RAB30 0.001 1.60 REG4 0.018 1.58 RELA 0.001 1.62 RFX1 0.020 1.43 RGS10 <.001 1.71 SCUBE2 0.009 1.48 SEPT9 <.001 3.91 SH3RF2 0.004 1.48 SH3YL1 <.001 1.87 SHH <.001 2.45 SIM2 <.001 1.74 SIPA1L1 0.021 1.35 SLC22A3 <.001 1.63 SLC44A1 <.001 1.65 SPINT1 0.017 1.39 TFDP1 0.005 1.75 TMPRSS2ERGA 0.002 14E5 TMPRSS2ERGB <.001 1.97 TRIM14 <.001 1.65 TSTA3 0.018 1.38 UAP1 0.046 1.39 UBE2G1 0.001 1.66 UGDH <.001 2.22 XRCCS <.001 1.66 ZMYND8 <.001 2.19

TABLE 9B Genes significantly (p < 0.05) associated with TMPRSS fusion status in the primary Gleason pattern with odds ratio (OR) < 1.0 (increased expression is negatively associated with TMPRSS fusion positivity) Official Symbol p-value Odds Ratio ABCC4 0.045 0.77 ABHD2 <.001 0.38 ACTR2 0.027 0.73 ADAMTS1 0.024 0.58 ADH5 <.001 0.58 AGTR2 0.016 0.64 AKAP1 0.013 0.70 AKT2 0.015 0.71 ALCAM <.001 0.45 ALDH1A2 0.004 0.70 ANPEP <.001 0.43 ANXA2 0.010 0.71 APC 0.036 0.73 APOC1 0.002 0.56 APOE <.001 0.44 ARF1 0.041 0.77 ATM 0.036 0.74 AURKB <.001 0.62 AZGP1 <.001 0.54 BBC3 0.030 0.74 BCL2 0.012 0.70 BIN1 0.021 0.74 BTG1 0.004 0.67 BTG3 0.003 0.63 C7 0.023 0.74 CADM1 0.007 0.69 CASP1 0.011 0.70 CAV1 0.011 0.71 CCND1 0.019 0.72 CCR1 0.022 0.73 CD44 <.001 0.57 CD68 <.001 0.54 CD82 0.002 0.66 CDH5 0.007 0.66 CDKN1A <.001 0.60 CDKN2B <.001 0.54 CDKN2C 0.012 0.72 CDKN3 0.037 0.77 CHN1 0.038 0.75 CKS2 <.001 0.48 COL11A1 0.017 0.72 COL1A1 <.001 0.59 COL1A2 0.001 0.62 COL3A1 0.027 0.73 COL4A1 0.043 0.76 COL5A1 0.039 0.74 COL5A2 0.026 0.73 COL6A1 0.008 0.66 COL6A3 <.001 0.59 COL8A1 0.022 0.74 CSF1 0.011 0.70 CTNNB1 0.021 0.69 CTSB <.001 0.62 CTSD 0.036 0.68 CTSK 0.007 0.70 CTSS 0.002 0.64 CXCL12 <.001 0.48 CXCR4 0.005 0.68 CXCR7 0.046 0.76 CYR61 0.004 0.65 DAP 0.002 0.64 DARC 0.021 0.73 DDR2 0.021 0.73 DHRS9 <.001 0.52 DIAPH1 <.001 0.56 DICER1 0.029 0.75 DLC1 0.013 0.72 DLGAP1 <.001 0.60 DLL4 <.001 0.57 DPT 0.006 0.68 DUSP1 0.012 0.68 DUSP6 0.001 0.62 DVL1 0.037 0.75 EFNB2 <.001 0.32 EGR1 0.003 0.65 ELK4 <.001 0.60 ERBB2 <.001 0.61 ERBB3 0.045 0.76 ESR2 0.010 0.70 ETV1 0.042 0.74 FABP5 <.001 0.21 FAM13C 0.006 0.67 FCGR3A 0.018 0.72 FGF17 0.009 0.71 FGF6 0.011 0.70 FGF7 0.003 0.63 FN1 0.006 0.69 FOS 0.035 0.74 FOXP3 0.010 0.71 GABRG2 0.029 0.74 GADD45B 0.003 0.63 GDF15 <.001 0.54 GPM6B 0.004 0.67 GPNMB 0.001 0.62 GSN 0.009 0.69 HLA-G 0.050 0.74 HLF 0.018 0.74 HPS1 <.001 0.48 HSD17B3 0.003 0.60 HSD17B4 <.001 0.56 HSPB1 <.001 0.38 HSPB2 0.002 0.62 IFI30 0.049 0.75 IFNG 0.006 0.64 IGF1 0.016 0.73 IGF2 0.001 0.57 IGFBP2 <.001 0.51 IGFBP3 <.001 0.59 IGFBP6 <.001 0.57 IL10 <.001 0.62 IL17A 0.012 0.63 IL1A 0.011 0.59 IL2 0.001 0.63 IL6ST <.001 0.52 INSL4 0.014 0.71 ITGA1 0.009 0.69 ITGA4 0.007 0.68 JUN <.001 0.59 KIT <.001 0.64 KRT76 0.016 0.70 LAG3 0.002 0.63 LAPTM5 <.001 0.58 LGALS3 <.001 0.53 LTBP2 0.011 0.71 LUM 0.012 0.70 MAOA 0.020 0.73 MAP4K4 0.007 0.68 MGST1 <.001 0.54 MMP2 <.001 0.61 MPPED2 <.001 0.45 MRC1 0.005 0.67 MTPN 0.002 0.56 MTSS1 <.001 0.53 MVP 0.009 0.72 MYBPC1 <.001 0.51 MYLK3 0.001 0.58 NCAM1 <.001 0.59 NCAPD3 <.001 0.40 NCOR1 0.004 0.69 NFKBIA <.001 0.63 NNMT 0.006 0.66 NPBWR1 0.027 0.67 OAZ1 0.049 0.64 OLFML3 <.001 0.56 OSM <.001 0.64 PAGE1 0.012 0.52 PDGFRB 0.016 0.73 PECAM1 <.001 0.55 PGR 0.048 0.77 PIK3CA <.001 0.55 PIK3CG 0.008 0.71 PLAU 0.044 0.76 PLK1 0.006 0.68 PLOD2 0.013 0.71 PLP2 0.024 0.73 PNLIPRP2 0.009 0.70 PPAP2B <.001 0.62 PRKAR2B <.001 0.61 PRKCB 0.044 0.76 PROS1 0.005 0.67 PTEN <.001 0.47 PTGER3 0.007 0.69 PTH1R 0.011 0.70 PTK2B <.001 0.61 PTPN1 0.028 0.73 RAB27A <.001 0.21 RAD51 <.001 0.51 RAD9A 0.030 0.75 RARB <.001 0.62 RASSF1 0.038 0.76 RECK 0.009 0.62 RHOB 0.004 0.64 RHOC <.001 0.56 RLN1 <.001 0.30 RND3 0.014 0.72 S100P 0.002 0.66 SDC2 <.001 0.61 SEMA3A 0.001 0.64 SMAD4 <.001 0.64 SPARC <.001 0.59 SPARCL1 <.001 0.56 SPINK1 <.001 0.26 SRD5A1 0.039 0.76 STAT1 0.026 0.74 STS 0.006 0.64 SULF1 <.001 0.53 TFF3 <.001 0.19 TGFA 0.002 0.65 TGFB1I1 0.040 0.77 TGFB2 0.003 0.66 TGFB3 <.001 0.54 TGFBR2 <.001 0.61 THY1 <.001 0.63 TIMP2 0.004 0.66 TIMP3 <.001 0.60 TMPRSS2 <.001 0.40 TNFSF11 0.026 0.63 TPD52 0.002 0.64 TRAM1 <.001 0.45 TRPC6 0.002 0.64 TUBB2A <.001 0.49 VCL <.001 0.57 VEGFB 0.033 0.73 VEGFC <.001 0.61 VIM 0.012 0.69 WISP1 0.030 0.75 WNT5A <.001 0.50

A molecular field effect was investigated, and determined that the expression levels of histologically normal-appearing cells adjacent to the tumor exhibited a molecular signature of prostate cancer. Tables 10A and 10B provide genes significantly associated (p<0.05), positively or negatively, with cRFI or bRFI in non-tumor samples. Table 10A is negatively associated with good prognosis, while increased expression of genes in Table 10B is positively associated with good prognosis.

TABLE 10A Genes significantly (p < 0.05) associated with cRFI or bRFI in Non-Tumor Samples with hazard ratio (HR) > 1.0 (increased expression is negatively associated with good prognosis) Official cRFI bRFI Symbol HR p-value HR p-value ALCAM 1.278 0.036 ASPN 1.309 0.032 BAG5 1.458 0.004 BRCA2 1.385 <.001 CACNA1D 1.329 0.035 CD164 1.339 0.020 CDKN2B 1.398 0.014 COL3A1 1.300 0.035 COL4A1 1.358 0.019 CTNND2 1.370 0.001 DARC 1.451 0.003 DICER1 1.345 <.001 DPP4 1.358 0.008 EFNB2 1.323 0.007 FASN 1.327 0.035 GHR 1.332 0.048 HSPA5 1.260 0.048 INHBA 1.558 <.001 KCNN2 1.264 0.045 KRT76 1.115 <.001 LAMC1 1.390 0.014 LAMC2 1.216 0.042 LIG3 1.313 0.030 MAOA 1.405 0.013 MCM6 1.307 0.036 MKI67 1.271 0.008 NEK2 1.312 0.016 NPBWR1 1.278 0.035 ODC1 1.320 0.010 PEX10 1.361 0.014 PGK1 1.488 0.004 PLA2G7 1.337 0.025 POSTN 1.306 0.043 PTK6 1.344 0.005 REG4 1.348 0.009 RGS7 1.144 0.047 SFRP4 1.394 0.009 TARP 1.412 0.011 TFF1 1.346 0.010 TGFBR2 1.310 0.035 THY1 1.300 0.038 TMPRSS2ERGA 1.333 <.001 TPD52 1.374 0.015 TRPC6 1.272 0.046 UBE2C 1.323 0.007 UHRF1 1.325 0.021

TABLE 10B Genes significantly (p < 0.05) associated with cRFI or bRFI in Non-Tumor Samples with hazard ratio (HR) < 1.0 (increased expression is positively associated with good prognosis) Official cRFI bRFI Symbol HR p-value HR p-value ABCA5 0.807 0.028 ABCC3 0.760 0.019 0.750 0.003 ABHD2 0.781 0.028 ADAM15 0.718 0.005 AKAP1 0.740 0.009 AMPD3 0.793 0.013 ANGPT2 0.752 0.027 ANXA2 0.776 0.035 APC 0.755 0.014 APRT 0.762 0.025 AR 0.752 0.015 ARHGDIB 0.753 <.001 BIN1 0.738 0.016 CADM1 0.711 0.004 CCNH 0.820 0.041 CCR1 0.749 0.007 CDK14 0.772 0.014 CDK3 0.819 0.044 CDKN1C 0.808 0.038 CHAF1A 0.634 0.002 0.779 0.045 CHN1 0.803 0.034 CHRAC1 0.751 0.014 0.779 0.021 COL5A1 0.736 0.012 COL5A2 0.762 0.013 COL6A1 0.757 0.032 COL6A3 0.757 0.019 CSK 0.663 <.001 0.698 <.001 CTSK 0.782 0.029 CXCL12 0.771 0.037 CXCR7 0.753 0.008 CYP3A5 0.790 0.035 DDIT4 0.725 0.017 DIAPH1 0.771 0.015 DLC1 0.744 0.004 0.807 0.015 DLGAP1 0.708 0.004 DUSP1 0.740 0.034 EDN1 0.742 0.010 EGR1 0.731 0.028 EIF3H 0.761 0.024 EIF4E 0.786 0.041 ERBB2 0.664 0.001 ERBB4 0.764 0.036 ERCC1 0.804 0.041 ESR2 0.757 0.025 EZH2 0.798 0.048 FAAH 0.798 0.042 FAM13C 0.764 0.012 FAM171B 0.755 0.005 FAM49B 0.811 0.043 FAM73A 0.778 0.015 FASLG 0.757 0.041 FGFR2 0.735 0.016 FOS 0.690 0.008 FYN 0.788 0.035 0.777 0.011 GPNMB 0.762 0.011 GSK3B 0.792 0.038 HGD 0.774 0.017 HIRIP3 0.802 0.033 HSP90AB1 0.753 0.013 HSPB1 0.764 0.021 HSPE1 0.668 0.001 IFI30 0.732 0.002 IGF2 0.747 0.006 IGFBP5 0.691 0.006 IL6ST 0.748 0.010 IL8 0.785 0.028 IMMT 0.708 <.001 ITGA6 0.747 0.008 ITGAV 0.792 0.016 ITGB3 0.814 0.034 ITPR3 0.769 0.009 JUN 0.655 0.005 KHDRBS3 0.764 0.012 KLF6 0.714 <.001 KLK2 0.813 0.048 LAMA4 0.702 0.009 LAMA5 0.744 0.011 LAPTM5 0.740 0.009 LGALS3 0.773 0.036 0.788 0.024 LIMS1 0.807 0.012 MAP3K5 0.815 0.034 MAP3K7 0.809 0.032 MAP4K4 0.735 0.018 0.761 0.010 MAPKAPK3 0.754 0.014 MICA 0.785 0.019 MTA1 0.808 0.043 MVP 0.691 0.001 MYLK3 0.730 0.039 MYO6 0.780 0.037 NCOA1 0.787 0.040 NCOR1 0.876 0.020 NDRG1 0.761 <.001 NFAT5 0.770 0.032 NFKBIA 0.799 0.018 NME2 0.753 0.005 NUP62 0.842 0.032 OAZ1 0.803 0.043 OLFML2B 0.745 0.023 OLFML3 0.743 0.009 OSM 0.726 0.018 PCA3 0.714 0.019 PECAM1 0.774 0.023 PIK3C2A 0.768 0.001 PIM1 0.725 0.011 PLOD2 0.713 0.008 PPP3CA 0.768 0.040 PROM1 0.482 <.001 PTEN 0.807 0.012 PTGS2 0.726 0.011 PTTG1 0.729 0.006 PYCARD 0.783 0.012 RAB30 0.730 0.002 RAGE 0.792 0.012 RFX1 0.789 0.016 0.792 0.010 RGS10 0.781 0.017 RUNX1 0.747 0.007 SDHC 0.827 0.036 SEC23A 0.752 0.010 SEPT9 0.889 0.006 SERPINA3 0.738 0.013 SLC25A21 0.788 0.045 SMARCD1 0.788 0.010 0.733 0.007 SMO 0.813 0.035 SRC 0.758 0.026 SRD5A2 0.738 0.005 ST5 0.767 0.022 STAT5A 0.784 0.039 TGFB2 0.771 0.027 TGFB3 0.752 0.036 THBS2 0.751 0.015 TNFRSF10B 0.739 0.010 TPX2 0.754 0.023 TRAF3IP2 0.774 0.015 TRAM1 0.868 <.001 0.880 <.001 TRIM14 0.785 0.047 TUBB2A 0.705 0.010 TYMP 0.778 0.024 UAP1 0.721 0.013 UTP23 0.763 0.007 0.826 0.018 VCL 0.837 0.040 VEGFA 0.755 0.009 WDR19 0.724 0.005 YBX1 0.786 0.027 ZFP36 0.744 0.032 ZNF827 0.770 0.043

Table 11 provides genes that are significantly associated (p<0.05) with cRFI or bRFI after adjustment for Gleason pattern or highest Gleason pattern.

TABLE 11 Genes significantly (p < 0.05) associated with cRFI or bRFI after adjustment for Gleason pattern in the primary Gleason pattern or highest Gleason pattern Some HR <= 1.0 and some HR >1.0 TABLE 11 cRFI bRFI bRFI Official Highest Pattern Primary Pattern Highest Pattern Symbol HR p-value HR p-value HR p-value HSPA5 0.710 0.009 1.288 0.030 ODC1 0.741 0.026 1.343 0.004 1.261 0.046

Tables 12A and 12B provide genes that are significantly associated (p<0.05) with prostate cancer specific survival (PCSS) in the primary Gleason pattern. Increased expression of genes in Table 12A is negatively associated with good prognosis, while increased expression of genes in Table 12B is positively associated with good prognosis.

TABLE 12A Genes significantly (p < 0.05) associated with prostate cancer specific survival (PCSS) in the Primary Gleason Pattern HR > 1.0 (Increased expression is negatively associated with good prognosis) Official Symbol HR p-value AKR1C3 1.476 0.016 ANLN 1.517 0.006 APOC1 1.285 0.016 APOE 1.490 0.024 ASPN 3.055 <.001 ATP5E 1.788 0.012 AURKB 1.439 0.008 BGN 2.640 <.001 BIRC5 1.611 <.001 BMP6 1.490 0.021 BRCA1 1.418 0.036 CCNB1 1.497 0.021 CD276 1.668 0.005 CDC20 1.730 <.001 CDH11 1.565 0.017 CDH7 1.553 0.007 CDKN2B 1.751 0.003 CDKN2C 1.993 0.013 CDKN3 1.404 0.008 CENPF 2.031 <.001 CHAF1A 1.376 0.011 CKS2 1.499 0.031 COL1A1 2.574 <.001 COL1A2 1.607 0.011 COL3A1 2.382 <.001 COL4A1 1.970 <.001 COL5A2 1.938 0.002 COL8A1 2.245 <.001 CTHRC1 2.085 <.001 CXCR4 1.783 0.007 DDIT4 1.535 0.030 DYNLL1 1.719 0.001 F2R 2.169 <.001 FAM171B 1.430 0.044 FAP 1.993 0.002 FCGR3A 2.099 <.001 FN1 1.537 0.024 GPR68 1.520 0.018 GREM1 1.942 <.001 IFI30 1.482 0.048 IGFBP3 1.513 0.027 INHBA 3.060 <.001 KIF4A 1.355 0.001 KLK14 1.187 0.004 LAPTM5 1.613 0.006 LTBP2 2.018 <.001 MMP11 1.869 <.001 MYBL2 1.737 0.013 NEK2 1.445 0.028 NOX4 2.049 <.001 OLFML2B 1.497 0.023 PLK1 1.603 0.006 POSTN 2.585 <.001 PPFIA3 1.502 0.012 PTK6 1.527 0.009 PTTG1 1.382 0.029 RAD51 1.304 0.031 RGS7 1.251 <.001 RRM2 1.515 <.001 SAT1 1.607 0.004 SDC1 1.710 0.007 SESN3 1.399 0.045 SFRP4 2.384 <.001 SHMT2 1.949 0.003 SPARC 2.249 <.001 STMN1 1.748 0.021 SULF1 1.803 0.004 THBS2 2.576 <.001 THY1 1.908 0.001 TK1 1.394 0.004 TOP2A 2.119 <.001 TPX2 2.074 0.042 UBE2C 1.598 <.001 UGT2B15 1.363 0.016 UHRF1 1.642 0.001 ZWINT 1.570 0.010

TABLE 12B Genes significantly (p < 0.05) associated with prostate cancer specific survival (PCSS) in the Primary Gleason Pattern HR < 1.0 (Increased expression is positively associated with good prognosis) Official Symbol HR p-value AAMP 0.649 0.040 ABCA5 0.777 0.015 ABCG2 0.715 0.037 ACOX2 0.673 0.016 ADH5 0.522 <.001 ALDH1A2 0.561 <.001 AMACR 0.693 0.029 AMPD3 0.750 0.049 ANPEP 0.531 <.001 ATXN1 0.640 0.011 AXIN2 0.657 0.002 AZGP1 0.617 <.001 BDKRB1 0.553 0.032 BIN1 0.658 <.001 BTRC 0.716 0.011 C7 0.531 <.001 CADM1 0.646 0.015 CASP7 0.538 0.029 CCNH 0.674 0.001 CD164 0.606 <.001 CD44 0.687 0.016 CDK3 0.733 0.039 CHN1 0.653 0.014 COL6A1 0.681 0.015 CSF1 0.675 0.019 CSRP1 0.711 0.007 CXCL12 0.650 0.015 CYP3A5 0.507 <.001 CYR61 0.569 0.007 DLGAP1 0.654 0.004 DNM3 0.692 0.010 DPP4 0.544 <.001 DPT 0.543 <.001 DUSP1 0.660 0.050 DUSP6 0.699 0.033 EGR1 0.490 <.001 EGR3 0.561 <.001 EIF5 0.720 0.035 ERBB3 0.739 0.042 FAAH 0.636 0.010 FAM107A 0.541 <.001 FAM13C 0.526 <.001 FAS 0.689 0.030 FGF10 0.657 0.024 FKBP5 0.699 0.040 FLNC 0.742 0.036 FOS 0.556 0.005 FOXQ1 0.666 0.007 GADD45B 0.554 0.002 GDF15 0.659 0.009 GHR 0.683 0.027 GPM6B 0.666 0.005 GSN 0.646 0.006 GSTM1 0.672 0.006 GSTM2 0.514 <.001 HGD 0.771 0.039 HIRIP3 0.730 0.013 HK1 0.778 0.048 HLF 0.581 <.001 HNF1B 0.643 0.013 HSD17B10 0.742 0.029 IER3 0.717 0.049 IGF1 0.612 <.001 IGFBP6 0.578 0.003 IL2 0.528 0.010 IL6ST 0.574 <.001 IL8 0.540 0.001 ING5 0.688 0.015 ITGA6 0.710 0.005 ITGA7 0.676 0.033 JUN 0.506 0.001 KIT 0.628 0.047 KLK1 0.523 0.002 KLK2 0.581 <.001 KLK3 0.676 <.001 KRT15 0.684 0.005 KRT18 0.536 <.001 KRT5 0.673 0.004 KRT8 0.613 0.006 LAMB3 0.740 0.027 LGALS3 0.678 0.007 MGST1 0.640 0.002 MPPED2 0.629 <.001 MTSS1 0.705 0.041 MYBPC1 0.534 <.001 NCAPD3 0.519 <.001 NFAT5 0.536 <.001 NRG1 0.467 0.007 OLFML3 0.646 0.001 OMD 0.630 0.006 OR51E2 0.762 0.017 PAGE4 0.518 <.001 PCA3 0.581 <.001 PGF 0.705 0.038 PPAP2B 0.568 <.001 PPP1R12A 0.694 0.017 PRIMA1 0.678 0.014 PRKCA 0.632 0.001 PRKCB 0.692 0.028 PROM1 0.393 0.017 PTEN 0.689 0.002 PTGS2 0.611 0.004 PTH1R 0.629 0.031 RAB27A 0.721 0.046 RND3 0.678 0.029 RNF114 0.714 0.035 SDHC 0.590 <.001 SERPINA3 0.710 0.050 SH3RF2 0.570 0.005 SLC22A3 0.517 <.001 SMAD4 0.528 <.001 SMO 0.751 0.026 SRC 0.667 0.004 SRD5A2 0.488 <.001 STAT5B 0.700 0.040 SVIL 0.694 0.024 TFF3 0.701 0.045 TGFB1I1 0.670 0.029 TGFB2 0.646 0.010 TNFRSF10B 0.685 0.014 TNFSF10 0.532 <.001 TPM2 0.623 0.005 TRO 0.767 0.049 TUBB2A 0.613 0.003 VEGFB 0.780 0.034 ZFP36 0.576 0.001 ZNF827 0.644 0.014

Analysis of gene expression and upgrading/upstaging was based on univariate ordinal logistic regression models using weighted maximum likelihood estimators for each gene in the gene list (727 test genes and 5 reference genes). P-values were generated using a Wald test of the null hypothesis that the odds ratio (OR) is one. Both unadjusted p-values and the q-value (smallest FDR at which the hypothesis test in question is rejected) were reported. Un-adjusted p-values <0.05 were considered statistically significant. Since two tumor specimens were selected for each patient, this analysis was performed using the 2 specimens from each patient as follows: (1) analysis using the primary Gleason pattern specimen from each patient (Specimens A1 and B2 as described in Table 2); and (2) analysis using the highest Gleason pattern specimen from each patient (Specimens A1 and B1 as described in Table 2). 200 genes were found to be significantly associated (p<0.05) with upgrading/upstaging in the primary Gleason pattern sample (PGP) and 203 genes were found to be significantly associated (p<0.05) with upgrading/upstaging in the highest Gleason pattern sample (HGP).

Tables 13A and 13B provide genes significantly associated (p<0.05), positively or negatively, with upgrading/upstaging in the primary and/or highest Gleason pattern. Increased expression of genes in Table 13A is positively associated with higher risk of upgrading/upstaging (poor prognosis), while increased expression of genes in Table 13B is negatively associated with risk of upgrading/upstaging (good prognosis).

TABLE 13A Genes significantly (p < 0.05) associated with upgrading/upstaging in the Primary Gleason Pattern (PGP) and Highest Gleason Pattern (HGP) OR > 1.0 (Increased expression is positively associated with higher risk of upgrading/upstaging (poor prognosis)) PGP HGP Gene OR p-value OR p-value ALCAM 1.52 0.0179 1.50 0.0184 ANLN 1.36 0.0451  .  . APOE 1.42 0.0278 1.50 0.0140 ASPN 1.60 0.0027 2.06 0.0001 AURKA 1.47 0.0108  .  . AURKB  .  . 1.52 0.0070 BAX  .  . 1.48 0.0095 BGN 1.58 0.0095 1.73 0.0034 BIRC5 1.38 0.0415  .  . BMP6 1.51 0.0091 1.59 0.0071 BUB1 1.38 0.0471 1.59 0.0068 CACNA1D 1.36 0.0474 1.52 0.0078 CASP7  .  . 1.32 0.0450 CCNE2 1.54 0.0042  .  . CD276  .  . 1.44 0.0265 CDC20 1.35 0.0445 1.39 0.0225 CDKN2B  .  . 1.36 0.0415 CENPF 1.43 0.0172 1.48 0.0102 CLTC 1.59 0.0031 1.57 0.0038 COL1A1 1.58 0.0045 1.75 0.0008 COL3A1 1.45 0.0143 1.47 0.0131 COL8A1 1.40 0.0292 1.43 0.0258 CRISP3  .  . 1.40 0.0256 CTHRC1  .  . 1.56 0.0092 DBN1 1.43 0.0323 1.45 0.0163 DIAPH1 1.51 0.0088 1.58 0.0025 DICER1  .  . 1.40 0.0293 DIO2  .  . 1.49 0.0097 DVL1  .  . 1.53 0.0160 F2R 1.46 0.0346 1.63 0.0024 FAP 1.47 0.0136 1.74 0.0005 FCGR3A  .  . 1.42 0.0221 HPN  .  . 1.36 0.0468 HSD17B4  .  . 1.47 0.0151 HSPA8 1.65 0.0060 1.58 0.0074 IL11 1.50 0.0100 1.48 0.0113 IL1B 1.41 0.0359  .  . INHBA 1.56 0.0064 1.71 0.0042 KHDRBS3 1.43 0.0219 1.59 0.0045 KIF4A  .  . 1.50 0.0209 KPNA2 1.40 0.0366  .  . KRT2  .  . 1.37 0.0456 KRT75  .  . 1.44 0.0389 MANF  .  . 1.39 0.0429 MELK 1.74 0.0016  .  . MKI67 1.35 0.0408  .  . MMP11  .  . 1.56 0.0057 NOX4 1.49 0.0105 1.49 0.0138 PLAUR 1.44 0.0185  .  . PLK1  .  . 1.41 0.0246 PTK6  .  . 1.36 0.0391 RAD51  .  . 1.39 0.0300 RAF1  .  . 1.58 0.0036 RRM2 1.57 0.0080  .  . SESN3 1.33 0.0465  .  . SFRP4 2.33 <0.0001 2.51 0.0015 SKIL 1.44 0.0288 1.40 0.0368 SOX4 1.50 0.0087 1.59 0.0022 SPINK1 1.52 0.0058  .  . SPP1  .  . 1.42 0.0224 THBS2  .  . 1.36 0.0461 TK1  .  . 1.38 0.0283 TOP2A 1.85 0.0001 1.66 0.0011 TPD52 1.78 0.0003 1.64 0.0041 TPX2 1.70 0.0010  .  . UBE2G1 1.38 0.0491  .  . UBE2T 1.37 0.0425 1.46 0.0162 UHRF1  .  . 1.43 0.0164 VCPIP1  .  . 1.37 0.0458

TABLE 13B Genes significantly (p < 0.05) associated with upgrading/upstaging in the Primary Gleason Pattern (PGP) and Highest Gleason Pattern (HGP) OR < 1.0 (Increased expression is negatively associated with higher risk of upgrading/upstaging (good prognosis)) PGP HGP Gene OR p-value OR p-value ABCC3  .    . 0.70   0.0216 ABCC8 0.66   0.0121  .    . ABCG2 0.67   0.0208 0.61   0.0071 ACE  .    . 0.73   0.0442 ACOX2 0.46   0.0000 0.49   0.0001 ADH5 0.69   0.0284 0.59   0.0047 AIG1  .    . 0.60   0.0045 AKR1C1  .    . 0.66   0.0095 ALDH1A2 0.36 <0.0001 0.36 <0.0001 ALKBH3 0.70   0.0281 0.61   0.0056 ANPEP  .    . 0.68   0.0109 ANXA2 0.73   0.0411 0.66   0.0080 APC  .    . 0.68   0.0223 ATXN1  .    . 0.70   0.0188 AXIN2 0.60   0.0072 0.68   0.0204 AZGP1 0.66   0.0089 0.57   0.0028 BCL2 .    . 0.71   0.0182 BIN1 0.55   0.0005  .    . BTRC 0.69   0.0397 0.70   0.0251 C7 0.53   0.0002 0.51 <0.0001 CADM1 0.57   0.0012 0.60   0.0032 CASP1 0.64   0.0035 0.72   0.0210 CAV1 0.64   0.0097 0.59   0.0032 CAV2  .    . 0.58   0.0107 CD164  .    . 0.69   0.0260 CD82 0.67   0.0157 0.69   0.0167 CDH1 0.61   0.0012 0.70   0.0210 CDK14 0.70   0.0354  .    . CDK3  .    . 0.72   0.0267 CDKN1C 0.61   0.0036 0.56   0.0003 CHN1 0.71   0.0214  .    . COL6A1 0.62   0.0125 0.60   0.0050 COL6A3 0.65   0.0080 0.68   0.0181 CSRP1 0.43   0.0001 0.40   0.0002 CTSB 0.66   0.0042 0.67   0.0051 CTSD 0.64   0.0355  .    . CTSK 0.69   0.0171  .    . CTSL1 0.72   0.0402  .    . CUL1 0.61   0.0024 0.70   0.0120 CXCL12 0.69   0.0287 0.63   0.0053 CYP3A5 0.68   0.0099 0.62   0.0026 DDR2 0.68   0.0324 0.62   0.0050 DES 0.54   0.0013 0.46   0.0002 DHX9 0.67   0.0164  .    . DLGAP1  .    . 0.66   0.0086 DPP4 0.69   0.0438 0.69   0.0132 DPT 0.59   0.0034 0.51   0.0005 DUSP1  .    . 0.67   0.0214 EDN1  .    . 0.66   0.0073 EDNRA 0.66   0.0148 0.54   0.0005 EIF2C2  .    . 0.65   0.0087 ELK4 0.55   0.0003 0.58   0.0013 ENPP2 0.65   0.0128 0.59   0.0007 EPHA3 0.71   0.0397 0.73   0.0455 EPHB2 0.60   0.0014  .    . EPHB4 0.73   0.0418  .    . EPHX3  .    . 0.71   0.0419 ERCC1 0.71   0.0325  .    . FAM107A 0.56   0.0008 0.55   0.0011 FAM13C 0.68   0.0276 0.55   0.0001 FAS 0.72   0.0404  .    . FBN1 0.72   0.0395  .    . FBXW7 0.69   0.0417  .    . FGF10 0.59   0.0024 0.51   0.0001 FGF7 0.51   0.0002 0.56   0.0007 FGFR2 0.54   0.0004 0.47 <0.0001 FLNA 0.58   0.0036 0.50   0.0002 FLNC 0.45   0.0001 0.40 <0.0001 FLT4 0.61   0.0045  .    . FOXO1 0.55   0.0005 0.53   0.0005 FOXP3 0.71   0.0275 0.72   0.0354 GHR 0.59   0.0074 0.53   0.0001 GNRH1 0.72   0.0386  .    . GPM6B 0.59   0.0024 0.52   0.0002 GSN 0.65   0.0107 0.65   0.0098 GSTM1 0.44 <0.0001 0.43 <0.0001 GSTM2 0.42 <0.0001 0.39 <0.0001 HLF 0.46 <0.0001 0.47   0.0001 HPS1 0.64   0.0069 0.69   0.0134 HSPA5 0.68   0.0113  .    . HSPB2 0.61   0.0061 0.55   0.0004 HSPG2 0.70   0.0359  .    . ID3  .    . 0.70   0.0245 IGF1 0.45 <0.0001 0.50   0.0005 IGF2 0.67   0.0200 0.68   0.0152 IGFBP2 0.59   0.0017 0.69   0.0250 IGFBP6 0.49 <0.0001 0.64   0.0092 IL6ST 0.56   0.0009 0.60   0.0012 ILK 0.51   0.0010 0.49   0.0004 ITGA1 0.58   0.0020 0.58   0.0016 ITGA3 0.71   0.0286 0.70   0.0221 ITGA5  .    . 0.69   0.0183 ITGA7 0.56   0.0035 0.42 <0.0001 ITGB1 0.63   0.0095 0.68   0.0267 ITGB3 0.62   0.0043 0.62   0.0040 ITPR1 0.62   0.0032  .    . JUN 0.73   0.0490 0.68   0.0152 KIT 0.55   0.0003 0.57   0.0005 KLC1  .    . 0.70   0.0248 KLK1  .    . 0.60   0.0059 KRT15 0.58   0.0009 0.45 <0.0001 KRT5 0.70   0.0262 0.59   0.0008 LAMA4 0.56   0.0359 0.68   0.0498 LAMB3  .    . 0.60   0.0017 LGALS3 0.58   0.0007 0.56   0.0012 LRP1 0.69   0.0176  .    . MAP3K7 0.70   0.0233 0.73   0.0392 MCM3 0.72   0.0320  .    . MMP2 0.66   0.0045 0.60   0.0009 MMP7 0.61   0.0015 0.65   0.0032 MMP9 0.64   0.0057 0.72   0.0399 MPPED2 0.72   0.0392 0.63   0.0042 MTA1  .    . 0.68   0.0095 MTSS1 0.58   0.0007 0.71   0.0442 MVP 0.57   0.0003 0.70   0.0152 MYBPC1  .    . 0.70   0.0359 NCAM1 0.63   0.0104 0.64   0.0080 NCAPD3 0.67   0.0145 0.64   0.0128 NEXN 0.54   0.0004 0.55   0.0003 NFAT5 0.72   0.0320 0.70   0.0177 NUDT6 0.66   0.0102  .    . OLFML3 0.56   0.0035 0.51   0.0011 OMD 0.61   0.0011 0.73   0.0357 PAGE4 0.42 <0.0001 0.36 <0.0001 PAK6 0.72   0.0335  .    . PCDHGB7 0.70   0.0262 0.55   0.0004 PGF 0.72   0.0358 0.71   0.0270 PLP2 0.66   0.0088 0.63   0.0041 PPAP2B 0.44 <0.0001 0.50   0.0001 PPP1R12A 0.45   0.0001 0.40 <0.0001 PRIMA1  .    . 0.63   0.0102 PRKAR2B 0.71   0.0226  .    . PRKCA 0.34 <0.0001 0.42 <0.0001 PRKCB 0.66   0.0120 0.49 <0.0001 PROM1 0.61   0.0030  .    . PTEN 0.59   0.0008 0.55   0.0001 PTGER3 0.67   0.0293  .    . PTH1R 0.69   0.0259 0.71   0.0327 PTK2 0.75   0.0461  .    . PTK2B 0.70   0.0244 0.74   0.0388 PYCARD 0.73   0.0339 0.67   0.0100 RAD9A 0.64   0.0124  .    . RARB 0.67   0.0088 0.65   0.0116 RGS10 0.70   0.0219  .    . RHOB  .    . 0.72   0.0475 RND3  .    . 0.67   0.0231 SDHC 0.72   0.0443  .    . SEC23A 0.66   0.0101 0.53   0.0003 SEMA3A 0.51   0.0001 0.69   0.0222 SH3RF2 0.55   0.0002 0.54   0.0002 SLC22A3 0.48   0.0001 0.50   0.0058 SMAD4 0.49   0.0001 0.50   0.0003 SMARCC2 0.59   0.0028 0.65   0.0052 SMO 0.60   0.0048 0.52 <0.0001 SORBS1 0.56   0.0024 0.48   0.0002 SPARCL1 0.43   0.0001 0.50   0.0001 SRD5A2 0.26 <0.0001 0.31 <0.0001 ST5 0.63   0.0103 0.52   0.0006 STAT5A 0.60   0.0015 0.61   0.0037 STAT5B 0.54   0.0005 0.57   0.0008 SUMO1 0.65   0.0066 0.66   0.0320 SVIL 0.52   0.0067 0.46   0.0003 TGFB1I1 0.44   0.0001 0.43   0.0000 TGFB2 0.55   0.0007 0.58   0.0016 TGFB3 0.57   0.0010 0.53   0.0005 TIMP1 0.72   0.0224  .    . TIMP2 0.68   0.0198 0.69   0.0206 TIMP3 0.67   0.0105 0.64   0.0065 TMPRSS2  .    . 0.72   0.0366 TNFRSF10A 0.71   0.0181  .    . TNFSF10 0.71   0.0284  .    . TOP2B 0.73   0.0432  .    . TP63 0.62   0.0014 0.50 <0.0001 TPM1 0.54   0.0007 0.52   0.0002 TPM2 0.41 <0.0001 0.40 <0.0001 TPP2 0.65   0.0122  .    . TRA2A 0.72   0.0318  .    . TRAF3IP2 0.62   0.0064 0.59   0.0053 TRO 0.57   0.0003 0.51   0.0001 VCL 0.52   0.0005 0.52   0.0004 VIM 0.65   0.0072 0.65   0.0045 WDR19 0.66   0.0097  .    . WFDC1 0.58   0.0023 0.60   0.0026 ZFHX3 0.69   0.0144 0.62   0.0046 ZNF827 0.62   0.0030 0.53   0.0001

Example 3: Identification of MicroRNAs Associated with Clinical Recurrence and Death Due to Prostate Cancer

MicroRNAs function by binding to portions of messenger RNA (mRNA) and changing how frequently the mRNA is translated into protein. They can also influence the turnover of mRNA and thus how long the mRNA remains intact in the cell. Since microRNAs function primarily as an adjunct to mRNA, this study evaluated the joint prognostic value of microRNA expression and gene (mRNA) expression. Since the expression of certain microRNAs may be a surrogate for expression of genes that are not in the assessed panel, we also evaluated the prognostic value of microRNA expression by itself.

Patients and Samples

Samples from the 127 patients with clinical recurrence and 374 patients without clinical recurrence after radical prostatectomy described in Example 2 were used in this study. The final analysis set comprised 416 samples from patients in which both gene expression and microRNA expression were successfully assayed. Of these, 106 patients exhibited clinical recurrence and 310 did not have clinical recurrence. Tissue samples were taken from each prostate sample representing (1) the primary Gleason pattern in the sample, and (2) the highest Gleason pattern in the sample. In addition, a sample of histologically normal-appearing tissue adjacent to the tumor (NAT) was taken. The number of patients in the analysis set for each tissue type and the number of them who experienced clinical recurrence or death due to prostate cancer are shown in Table 14.

TABLE 14 Number of Patients and Events in Analysis Set Clinical Deaths Due to Patients Recurrences Prostate Cancer Primary Gleason 416 106 36 Pattern Tumor Tissue Highest Gleason 405 102 36 Pattern Tumor Tissue Normal Adjacent 364  81 29 Tissue

Assay Method

Expression of 76 test microRNAs and 5 reference microRNAs were determined from RNA extracted from fixed paraffin-embedded (FPE) tissue. MicroRNA expression in all three tissue type was quantified by reverse transcriptase polymerase chain reaction (RT-PCR) using the crossing point (C_(p)) obtained from the Taqman® MicroRNA Assay kit (Applied Biosystems, Inc., Carlsbad, Calif.).

Statistical Analysis

Using univariate proportional hazards regression (Cox DR, Journal of the Royal Statistical Society, Series B 34:187-220, 1972), applying the sampling weights from the cohort sampling design, and using variance estimation based on the Lin and Wei method (Lin and Wei, Journal of the American Statistical Association 84:1074-1078, 1989), microRNA expression, normalized by the average expression for the 5 reference microRNAs hsa-miR-106a, hsa-miR-146b-5p, hsa-miR-191, hsa-miR-19b, and hsa-miR-92a, and reference-normalized gene expression of the 733 genes (including the reference genes) discussed above, were assessed for association with clinical recurrence and death due to prostate cancer. Standardized hazard ratios (the proportional change in the hazard associated with a change of one standard deviation in the covariate value) were calculated.

This analysis included the following classes of predictors:

1. MicroRNAs alone

2. MicroRNA-gene pairs Tier 1

3. MicroRNA-gene pairs Tier 2

4. MicroRNA-gene pairs Tier 3

5. All other microRNA-gene pairs Tier 4

The four tiers were pre-determined based on the likelihood (Tier 1 representing the highest likelihood) that the gene-microRNA pair functionally interacted or that the microRNA was related to prostate cancer based on a review of the literature and existing microarray data sets.

False discovery rates (FDR) (Benjamini and Hochberg, Journal of the Royal Statistical Society, Series B 57:289-300, 1995) were assessed using Efron's separate class methodology (Efron, Annals of Applied Statistics 2:197-223, 2008). The false discovery rate is the expected proportion of the rejected null hypotheses that are rejected incorrectly (and thus are false discoveries). Efron's methodology allows separate FDR assessment (q-values) (Storey, Journal of the Royal Statistical Society, Series B 64:479-498, 2002) within each class while utilizing the data from all the classes to improve the accuracy of the calculation. In this analysis, the q-value for a microRNA or microRNA-gene pair can be interpreted as the empirical Bayes probability that the microRNA or microRNA-gene pair identified as being associated with clinical outcome is in fact a false discovery given the data. The separate class approach was applied to a true discovery rate degree of association (TDRDA) analysis (Crager, Statistics in Medicine 29:33-45, 2010) to determine sets of microRNAs or microRNA-gene pairs that have standardized hazard ratio for clinical recurrence or prostate cancer-specific death of at least a specified amount while controlling the FDR at 10%. For each microRNA or microRNA-gene pair, a maximum lower bound (MLB) standardized hazard ratio was computed, showing the highest lower bound for which the microRNA or microRNA-gene pair was included in a TDRDA set with 10% FDR. Also calculated was an estimate of the true standardized hazard ratio corrected for regression to the mean (RM) that occurs in subsequent studies when the best predictors are selected from a long list (Crager, 2010 above). The RM-corrected estimate of the standardized hazard ratio is a reasonable estimate of what could be expected if the selected microRNA or microRNA-gene pair were studied in a separate, subsequent study.

These analyses were repeated adjusting for clinical and pathology covariates available at the time of patient biopsy: biopsy Gleason score, baseline PSA level, and clinical T-stage (T1-T2A vs. T2B or T2C) to assess whether the microRNAs or microRNA-gene pairs have predictive value independent of these clinical and pathology covariates.

Results

The analysis identified 21 microRNAs assayed from primary Gleason pattern tumor tissue that were associated with clinical recurrence of prostate cancer after radical prostatectomy, allowing a false discovery rate of 10% (Table 15). Results were similar for microRNAs assessed from highest Gleason pattern tumor tissue (Table 16), suggesting that the association of microRNA expression with clinical recurrence does not change markedly depending on the location within a tumor tissue sample. No microRNA assayed from normal adjacent tissue was associated with the risk of clinical recurrence at a false discovery rate of 10%. The sequences of the microRNAs listed in Tables 15-21 are shown in Table B.

TABLE 15 MicroRNAs Associated with Clinical Recurrence of Prostate Cancer Primary Gleason Pattern Tumor Tissue Absolute Standardized Hazard Ratio Direction Uncor- 95% Max. Lower RM- q-value^(a) of Asso- rected Confidence Bound Corrected MicroRNA p-value (FDR) ciation^(b) Estimate Interval @10% FDR Estimate^(c) hsa-miR-93 <0.0001 0.0% (+) 1.79 (1.38, 2.32) 1.19 1.51 hsa-miR-106b <0.0001 0.1% (+) 1.80 (1.38,2.34) 1.19 1.51 hsa-miR-30e-5p <0.0001 0.1% (−) 1.63 (1.30, 2.04) 1.18 1.46 hsa-miR-21 <0.0001 0.1% (+) 1.66 (1.31,2.09) 1.18 1.46 hsa-miR-133a <0.0001 0.1% (−) 1.72 (1.33, 2.21) 1.18 1.48 hsa-miR-449a <0.0001 0.1% (+) 1.56 (1.26, 1.92) 1.17 1.42 hsa-miR-30a 0.0001 0.1% (−) 1.56 (1.25, 1.94) 1.16 1.41 hsa-miR-182 0.0001 0.2% (+) 1.74 (1.31, 2.31) 1.17 1.45 hsa-miR-27a 0.0002 0.2% (+) 1.65 (1.27, 2.14) 1.16 1.43 hsa-miR-222 0.0006 0.5% (−) 1.47 (1.18, 1.84) 1.12 1.35 hsa-miR-103 0.0036 2.1% (+) 1.77 (1.21, 2.61) 1.12 1.36 hsa-miR-1 0.0037 2.2% (−) 1.32 (1.10, 1.60) 1.07 1.26 hsa-miR-145 0.0053 2.9% (−) 1.34 (1.09, 1.65) 1.07 1.27 hsa-miR-141 0.0060 3.2% (+) 1.43 (1.11, 1.84) 1.07 1.29 hsa-miR-92a 0.0104 4.8% (+) 1.32 (1.07, 1.64) 1.05 1.25 hsa-miR-22 0.0204 7.7% (+) 1.31 (1.03, 1.64) 1.03 1.23 hsa-miR-29b 0.0212 7.9% (+) 1.36 (1.03, 1.76) 1.03 1.24 hsa-miR-210 0.0223 8.2% (+) 1.33 (1.03, 1.70) 1.00 1.23 hsa-miR-486-5p 0.0267 9.4% (−) 1.25 (1.00, 1.53) 1.00 1.20 hsa-miR-19b 0.0280 9.7% (−) 1.24 (1.00, 1.50) 1.00 1.19 hsa-miR-205 0.0289 10.0% (−) 1.25 (1.00, 1.53) 1.00 1.20 ^(a)The q-value is the empirical Bayes probability that the microRNA's association with clinical recurrence is a false discovery, given the data. ^(b)Direction of association indicates where higher microRNA expression is associated with higher (+) or lower (−) risk of clinical recurrence. ^(c)RM: regression to the mean.

TABLE 16 MicroRNAs Associated with Clinical Recurrence of Prostate Cancer Highest Gleason Pattern Tumor Tissue Absolute Standardized Hazard Ratio Direction Uncor- 95% Max. Lower RM- q-value^(a) of Asso- rected Confidence Bound Corrected MicroRNA p-value (FDR) ciation^(b) Estimate Interval @10% FDR Estimate^(c) hsa-miR-93 <0.0001 0.0% (+) 1.91 (1.48, 2.47) 1.24 1.59 hsa-miR-449a <0.0001 0.0% (+) 1.75 (1.40, 2.18) 1.23 1.54 hsa-miR-205 <0.0001 0.0% (−) 1.53 (1.29, 1.81) 1.20 1.43 hsa-miR-19b <0.0001 0.0% (−) 1.37 (1.19, 1.57) 1.15 1.32 hsa-miR-106b <0.0001 0.0% (+) 1.84 (1.39, 2.42) 1.22 1.51 hsa-miR-21 <0.0001 0.0% (+) 1.68 (1.32, 2.15) 1.19 1.46 hsa-miR-30a 0.0005 0.4% (−) 1.44 (1.17, 1.76) 1.13 1.33 hsa-miR-30e-5p 0.0010 0.6% (−) 1.37 (1.14, 1.66) 1.11 1.30 hsa-miR-133a 0.0015 0.8% (−) 1.57 (1.19, 2.07) 1.13 1.36 hsa-miR-1 0.0016 0.8% (−) 1.42 (1.14, 1.77) 1.11 1.31 hsa-miR-103 0.0021 1.1% (+) 1.69 (1.21, 2.37) 1.13 1.37 hsa-miR-210 0.0024 1.2% (+) 1.43 (1.13, 1.79) 1.11 1.31 hsa-miR-182 0.0040 1.7% (+) 1.48 (1.13, 1.93) 1.11 1.31 hsa-miR-27a 0.0055 2.1% (+) 1.46 (1.12, 1.91) 1.09 1.30 hsa-miR-222 0.0093 3.2% (−) 1.38 (1.08, 1.77) 1.08 1.27 hsa-miR-331 0.0126 3.9% (+) 1.38 (1.07, 1.77) 1.07 1.26 hsa-miR-191* 0.0143 4.3% (+) 1.38 (1.06, 1.78) 1.07 1.26 hsa-miR-425 0.0151 4.5% (+) 1.40 (1.06, 1.83) 1.07 1.26 hsa-miR-31 0.0176 5.1% (−) 1.29 (1.04, 1.60) 1.05 1.22 hsa-miR-92a 0.0202 5.6% (+) 1.31 (1.03, 1.65) 1.05 1.23 hsa-miR-155 0.0302 7.6% (−) 1.32 (1.00, 1.69) 1.03 1.22 hsa-miR-22 0.0437 9.9% (+) 1.30 (1.00, 1.67) 1.00 1.21 ^(a)The q-value is the empirical Bayes probability that the microRNA's association with death due to prostate cancer is a false discovery, given the data. ^(b)Direction of association indicates where higher microRNA expression is associated with higher (+) or lower (−) risk of clinical recurrence. ^(c)RM: regression to the mean.

Table 17 shows microRNAs assayed from primary Gleason pattern tissue that were identified as being associated with the risk of prostate-cancer-specific death, with a false discovery rate of 10%. Table 18 shows the corresponding analysis for microRNAs assayed from highest Gleason pattern tissue. No microRNA assayed from normal adjacent tissue was associated with the risk of prostate-cancer-specific death at a false discovery rate of 10%.

TABLE 17 MicroRNAs Associated with Death Due to Prostate Cancer Primary Gleason Pattern Tumor Tissue Absolute Standardized Hazard Ratio Max. Lower Direction Uncor- 95% Bound RM- q-value^(a) of Asso- rected Confidence @10% Corrected MicroRNA p-value (FDR) ciation^(b) Estimate Interval FDR Estimate^(c) hsa-miR-30e-5p 0.0001 0.6% (−) 1.88 (1.37, 2.58) 1.15 1.46 hsa-miR-30a 0.0001 0.7% (−) 1.78 (1.33, 2.40) 1.14 1.44 hsa-miR-133a 0.0005 1.2% (−) 1.85 (1.31, 2.62) 1.13 1.41 hsa-miR-222 0.0006 1.4% (−) 1.65 (1.24, 2.20) 1.12 1.38 hsa-miR-106b 0.0024 2.7% (+) 1.85 (1.24, 2.75) 1.11 1.35 hsa-miR-1 0.0028 3.0% (−) 1.43 (1.13, 1.81) 1.08 1.30 hsa-miR-21 0.0034 3.3% (+) 1.63 (1.17, 2.25) 1.09 1.33 hsa-miR-93 0.0044 3.9% (+) 1.87 (1.21, 2.87) 1.09 1.32 hsa-miR-26a 0.0072 5.3% (−) 1.47 (1.11, 1.94) 1.07 1.29 hsa-miR-152 0.0090 6.0% (−) 1.46 (1.10, 1.95) 1.06 1.28 hsa-miR-331 0.0105 6.5% (+) 1.46 (1.09, 1.96) 1.05 1.27 hsa-miR-150 0.0159 8.3% (+) 1.51 (1.07, 2.10) 1.03 1.27 hsa-miR-27b 0.0160 8.3% (+) 1.97 (1.12, 3.42) 1.05 1.25 ^(a)The q-value is the empirical Bayes probability that the microRNA's association with death due to prostate cancer endpoint is a false discovery, given the data. ^(b)Direction of association indicates where higher microRNA expression is associated with higher (+) or lower (−) risk of death due to prostate cancer. ^(c)RM: regression to the mean.

TABLE 18 MicroRNAs Associated with Death Due to Prostate Cancer Highest Gleason Pattern Tumor Tissue Absolute Standardized Hazard Ratio Max. Lower Direction Uncor- 95% Bound RM- q-value^(a) of Asso- rected Confidence @10% Corrected MicroRNA p-value (FDR) ciation^(b) Estimate Interval FDR Estimate^(c) hsa-miR-27b 0.0016 6.1% (+) 2.66 (1.45, 4.88) 1.07 1.32 hsa-miR-21 0.0020 6.4% (+) 1.66 (1.21, 2.30) 1.05 1.34 hsa-miR-10a 0.0024 6.7% (+) 1.78 (1.23, 2.59) 1.05 1.34 hsa-miR-93 0.0024 6.7% (+) 1.83 (1.24, 2.71) 1.05 1.34 hsa-miR-106b 0.0028 6.8% (+) 1.79 (1.22, 2.63) 1.05 1.33 hsa-miR-150 0.0035 7.1% (+) 1.61 (1.17, 2.22) 1.05 1.32 hsa-miR-1 0.0104 9.0% (−) 1.52 (1.10, 2.09) 1.00 1.28 ^(a)The q-value is the empirical Bayes probability that the microRNA's association with clinical endpoint is a false discovery, given the data. ^(b)Direction of association indicates where higher microRNA expression is associated with higher (+) or lower (−) risk of death due to prostate cancer. ^(c)RM: regression to the mean.

Table 19 and Table 20 shows the microRNAs that can be identified as being associated with the risk of clinical recurrence while adjusting for the clinical and pathology covariates of biopsy Gleason score, baseline PSA level, and clinical T-stage. The distributions of these covariates are shown in FIG. 1. Fifteen (15) of the microRNAs identified in Table 15 are also present in Table 19, indicating that these microRNAs have predictive value for clinical recurrence that is independent of the Gleason score, baseline PSA, and clinical T-stage.

Two microRNAs assayed from primary Gleason pattern tumor tissue were found that had predictive value for death due to prostate cancer independent of Gleason score, baseline PSA, and clinical T-stage (Table 21).

TABLE 19 MicroRNAs Associated with Clinical Recurrence of Prostate Cancer Adjusting for Biopsy Gleason Score, Baseline PSA Level, and Clinical T-Stage Primary Gleason Pattern Tumor Tissue Absolute Standardized Hazard Ratio Max. Lower Direction Uncor- 95% Bound RM- q-value^(a) of Asso- rected Confidence @10% Corrected MicroRNA p-value (FDR) ciation^(b) Estimate Interval FDR Estimate^(c) hsa-miR-30e-5p <0.0001 0.0% (−) 1.80 (1.42, 2.27) 1.23 1.53 hsa-miR-30a <0.0001 0.0% (−) 1.75 (1.40, 2.19) 1.22 1.51 hsa-miR-93 <0.0001 0.1% (+) 1.70 (1.32, 2.20) 1.19 1.44 hsa-miR-449a 0.0001 0.1% (+) 1.54 (1.25, 1.91) 1.17 1.39 hsa-miR-133a 0.0001 0.1% (−) 1.58 (1.25, 2.00) 1.17 1.39 hsa-miR-27a 0.0002 0.1% (+) 1.66 (1.28, 2.16) 1.17 1.41 hsa-miR-21 0.0003 0.2% (+) 1.58 (1.23, 2.02) 1.16 1.38 hsa-miR-182 0.0005 0.3% (+) 1.56 (1.22, 1.99) 1.15 1.37 hsa-miR-106b 0.0008 0.5% (+) 1.57 (1.21, 2.05) 1.15 1.36 hsa-miR-222 0.0028 1.1% (−) 1.39 (1.12, 1.73) 1.11 1.28 hsa-miR-103 0.0048 1.7% (+) 1.69 (1.17, 2.43) 1.13 1.32 hsa-miR-486-5p 0.0059 2.0% (−) 1.34 (1.09, 1.65) 1.09 1.25 hsa-miR-1 0.0083 2.7% (−) 1.29 (1.07, 1.57) 1.07 1.23 hsa-miR-141 0.0088 2.8% (+) 1.43 (1.09, 1.87) 1.09 1.27 hsa-miR-200c 0.0116 3.4% (+) 1.39 (1.07, 1.79) 1.07 1.25 hsa-miR-145 0.0201 5.1% (−) 1.27 (1.03, 1.55) 1.05 1.20 hsa-miR-206 0.0329 7.2% (−) 1.40 (1.00, 1.91) 1.05 1.23 hsa-miR-29b 0.0476 9.4% (+) 1.30 (1.00, 1.69) 1.00 1.20 ^(a)The q-value is the empirical Bayes probability that the microRNA's association with clinical recurrence is a false discovery, given the data. ^(b)Direction of association indicates where higher microRNA expression is associated with higher (+) or lower (−) risk of clinical recurrence. ^(c)RM: regression to the mean.

TABLE 20 MicroRNAs Associated with Clinical Recurrence of Prostate Cancer Adjusting for Biopsy Gleason Score, Baseline PSA Level, and Clinical T-Stage Highest Gleason Pattern Tumor Tissue Absolute Standardized Hazard Ratio Max. Lower Direction Uncor- 95% Bound RM- q-value^(a) of Asso- rected Confidence @10% Corrected MicroRNA p-value (FDR) ciation^(b) Estimate Interval FDR Estimate^(c) hsa-miR-30a <0.0001 0.0% (−) 1.62 (1.32, 1.99) 1.20 1.43 hsa-miR-30e-5p <0.0001 0.0% (−) 1.53 (1.27, 1.85) 1.19 1.39 hsa-miR-93 <0.0001 0.0% (+) 1.76 (1.37, 2.26) 1.20 1.45 hsa-miR-205 <0.0001 0.0% (−) 1.47 (1.23, 1.74) 1.18 1.36 hsa-miR-449a 0.0001 0.1% (+) 1.62 (1.27, 2.07) 1.18 1.38 hsa-miR-106b 0.0003 0.2% (+) 1.65 (1.26, 2.16) 1.17 1.36 hsa-miR-133a 0.0005 0.2% (−) 1.51 (1.20, 1.90) 1.16 1.33 hsa-miR-1 0.0007 0.3% (−) 1.38 (1.15, 1.67) 1.13 1.28 hsa-miR-210 0.0045 1.2% (+) 1.35 (1.10, 1.67) 1.11 1.25 hsa-miR-182 0.0052 1.3% (+) 1.40 (1.10, 1.77) 1.11 1.26 hsa-miR-425 0.0066 1.6% (+) 1.48 (1.12, 1.96) 1.12 1.26 hsa-miR-155 0.0073 1.8% (−) 1.36 (1.09, 1.70) 1.10 1.24 hsa-miR-21 0.0091 2.1% (+) 1.42 (1.09, 1.84) 1.10 1.25 hsa-miR-222 0.0125 2.7% (−) 1.34 (1.06, 1.69) 1.09 1.23 hsa-miR-27a 0.0132 2.8% (+) 1.40 (1.07, 1.84) 1.09 1.23 hsa-miR-191* 0.0150 3.0% (+) 1.37 (1.06, 1.76) 1.09 1.23 hsa-miR-103 0.0180 3.4% (+) 1.45 (1.06, 1.98) 1.09 1.23 hsa-miR-31 0.0252 4.3% (−) 1.27 (1.00, 1.57) 1.07 1.19 hsa-miR-19b 0.0266 4.5% (−) 1.29 (1.00, 1.63) 1.07 1.20 hsa-miR-99a 0.0310 5.0% (−) 1.26 (1.00, 1.56) 1.06 1.18 hsa-miR-92a 0.0348 5.4% (+) 1.31 (1.00, 1.69) 1.06 1.19 hsa-miR-146b-5p 0.0386 5.8% (−) 1.29 (1.00, 1.65) 1.06 1.19 hsa-miR-145 0.0787 9.7% (−) 1.23 (1.00, 1.55) 1.00 1.15 ^(a)The q-value is the empirical Bayes probability that the microRNA's association with clinical clinical recurrence is a false discovery, given the data. ^(b)Direction of association indicates where higher microRNA expression is associated with higher (+) or lower (−) risk of clinical recurrence. ^(c)RM: regression to the mean.

TABLE 21 MicroRNAs Associated with Death Due to Prostate Cancer Adjusting for Biopsy Gleason Score, Baseline PSA Level, and Clinical T-Stage Primary Gleason Pattern Tumor Tissue Absolute Standardized Hazard Ratio Max. Lower Direction Uncor- 95% Bound RM- q-value^(a) of Asso- rected Confidence @10% Corrected MicroRNA p-value (FDR) ciation^(b) Estimate Interval FDR Estimate^(c) hsa-miR-30e-5p 0.0001 2.9% (−) 1.97 (1.40, 2.78) 1.09 1.39 hsa-miR-30a 0.0002 3.3% (−) 1.90 (1.36, 2.65) 1.08 1.38 ^(a)The q-value is the empirical Bayes probability that the microRNA's association with clinical recurrence is a false discovery, given the data. ^(b)Direction of association indicates where higher microRNA expression is associated with higher (+) or lower (−) risk of clinical recurrence. ^(c)RM: regression to the mean.

Accordingly, the normalized expression levels of hsa-miR-93; hsa-miR-106b; hsa-miR-21; hsa-miR-449a; hsa-miR-182; hsa-miR-27a; hsa-miR-103; hsa-miR-141; hsa-miR-92a; hsa-miR-22; hsa-miR-29b; hsa-miR-210; hsa-miR-331; hsa-miR-191; hsa-miR-425; and hsa-miR-200c are positively associated with an increased risk of recurrence; and hsa-miR-30e-5p; hsa-miR-133a; hsa-miR-30a; hsa-miR-222; hsa-miR-1; hsa-miR-145; hsa-miR-486-5p; hsa-miR-19b; hsa-miR-205; hsa-miR-31; hsa-miR-155; hsa-miR-206; hsa-miR-99a; and hsa-miR-146b-5p are negatively associated with an increased risk of recurrence.

Furthermore, the normalized expression levels of hsa-miR-106b; hsa-miR-21; hsa-miR-93; hsa-miR-331; hsa-miR-150; hsa-miR-27b; and hsa-miR-10a are positively associated with an increased risk of prostate cancer specific death; and the normalized expression levels of hsa-miR-30e-5p; hsa-miR-30a; hsa-miR-133a; hsa-miR-222; hsa-miR-1; hsa-miR-26a; and hsa-miR-152 are negatively associated with an increased risk of prostate cancer specific death.

Table 22 shows the number of microRNA-gene pairs that were grouped in each tier (Tiers 1-4) and the number and percentage of those that were predictive of clinical recurrence at a false discovery rate of 10%.

TABLE 22 Number of Pairs Total Predictive of Clinical Number of Recurrence at False MicroRNA- Discovery Rate 10% Tier Gene Pairs (%) Tier 1    80    46 (57.5%) Tier 2   719   591 (82.2%) Tier 3  3,850  2,792 (72.5%) Tier 4 54,724 38,264 (69.9%)

TABLE A SEQ SEQ Official Accession ID ID Symbol: Number: NO Forward Primer Sequence: NO Reverse Primer Sequence: AAMP NM_001087 1 GTGTGGCAGGTGGACACTAA 2 CTCCATCCACTCCAGGTCTC ABCA5 NM_172232 5 GGTATGGATCCCAAAGCCA 6 CAGCCCGCTTTCTGTTTTTA ABCB1 NM_000927 9 AAACACCACTGGAGCATTGA 10 CAAGCCTGGAACCTATAGCC ABCC1 NM_004996 13 TCATGGTGCCCGTCAATG 14 CGATTGTCTTTGCTCTTCATGTG ABCC3 NM_003786 17 TCATCCTGGCGATCTACTTCCT 18 CCGTTGAGTGGAATCAGCAA ABCC4 NM_005845 21 AGCGCCTGGAATCTACAACT 22 AGAGCCCCTGGAGAGAAGAT ABCC8 NM_000352 25 CGTCTGTCACTGTGGAGTGG 26 TGATCCGGTTTAGCAGGC ABCG2 NM_004827 29 GGTCTCAACGCCATCCTG 30 CTTGGATCTTTCCTTGCAGC ABHD2 NM_007011 33 GTAGTGGGTCTGCATGGATGT 34 TGAGGGTTGGCACTCAGG ACE NM_000789 37 CCGCTGTACGAGGATTTCA 38 CCGTGTCTGTGAAGCCGT ACOX2 NM_003500 41 ATGGAGGTGCCCAGAACAC 42 ACTCCGGGTAACTGTGGATG ACTR2 NM_005722 45 ATCCGCATTGAAGACCCA 46 ATCCGCTAGAACTGCACCAC ADAM15 NM_003815 49 GGCGGGATGTGGTAACAG 50 ATTTCTGGGCCTCCGAGT ADAMTS1 NM_006988 53 GGACAGGTGCAAGCTCATCTG 54 ATCTACAACCTTGGGCTGCAA ADH5 NM_000671 57 ATGCTGTCATCATTGTCACG 58 CTGCTTCCTTTCCCTTTCC AFAP1 NM_198595 61 GATGTCCATCCTTGAAACAGC 62 CAACCCTGATGCCTGGAG AGTR1 NM_000685 65 AGCATTGATCGATACCTGGC 66 CTACAAGCATTGTGCGTCG AGTR2 NM_000686 69 ACTGGCATAGGAAATGGTATCC 70 ATTGACTGGGTCTCTTTGCC AIG1 NM_016108 73 CGACGGTTCTGCCCTTTAT 74 TGCTCCTGCTGGGATACTG AKAP1 NM_003488 77 TGTGGTTGGAGATGAAGTGG 78 GTCTACCCACTGGGCAAGG AKR1C1 BC040210 81 GTGTGTGAAGCTGAATGATGG 82 CTCTGCAGGCGCATAGGT AKR1C3 NM_003739 85 GCTTTGCCTGATGTCTACCAGAA 86 GTCCAGTCACCGGCATAGAGA AKT1 NM_005163 89 CGCTTCTATGGCGCTGAGAT 90 TCCCGGTACACCACGTTCTT AKT2 NM_001626 93 TCCTGCCACCCTTCAAACC 94 GGCGGTAAATTCATCATCGAA AKT3 NM_005465 97 TTGTCTCTGCCTTGGACTATCTACA 98 CCAGCATTAGATTCTCCAACTTGA ALCAM NM_001627 101 GAGGAATATGGAATCCAAGGG 102 GTGGCGGAGATCAAGAGG ALDH18A1 NM_002860 105 GATGCAGCTGGAACCCAA 106 CTCCAGCTCAGTGGGGAA ALDH1A2 NM_170696 109 CACGTCTGTCCCTCTCTGCT 110 GACCGTGGCTCAACTTTGTAT ALKBH3 NM_139178 113 TCGCTTAGTCTGCACCTCAAC 114 TCTGAGCCCCAGTTTTTCC ALOX12 NM_000697 117 AGTTCCTCAATGGTGCCAAC 118 AGCACTAGCCTGGAGGGC ALOX5 NM_000698 121 GAGCTGCAGGACTTCGTGA 122 GAAGCCTGAGGACTTGCG AMACR NM_203382 125 GTCTCTGGGCTGTCAGCTTT 126 TGGGTATAAGATCCAGAACTTGC AMPD3 NM_000480 129 TGGTTCATCCAGCACAAGG 130 CATAAATCCGGGGCACCT ANGPT2 NM_001147 133 CCGTGAAAGCTGCTCTGTAA 134 TTGCAGTGGGAAGAACAGTC ANLN NM_018685 137 TGAAAGTCCAAAACCAGGAA 138 CAGAACCAAGGCTATCACCA ANPEP NM_001150 141 CCACCTTGGACCAAAGTAAAGC 142 TCTCAGCGTCACCTGGTAGGA ANXA2 NM_004039 145 CAAGACACTAAGGGCGACTACCA 146 CGTGTCGGGCTTCAGTCAT APC NM_000038 149 GGACAGCAGGAATGTGTTTC 150 ACCCACTCGATTTGTTTCTG APEX1 NM_001641 153 GATGAAGCCTTTCGCAAGTT 154 AGGTCTCCACACAGCACAAG APOC1 NM_001645 157 CCAGCCTGATAAAGGTCCTG 158 CACTCTGAATCCTTGCTGGA APOE NM_000041 161 GCCTCAAGAGCTGGTTCG 162 CCTGCACCTTCTCCACCA APRT NM_000485 165 GAGGTCCTGGAGTGCGTG 166 AGGTGCCAGCTTCTCCCT AQP2 NM_000486 169 GTGTGGGTGCCAGTCCTC 170 CCCTTCAGCCCTCTCAAAG AR NM_000044 173 CGACTTCACCGCACCTGAT 174 TGACACAAGTGGGACTGGGATA ARF1 NM_001658 177 CAGTAGAGATCCCCGCAACT 178 ACAAGCACATGGCTATGGAA ARHGAP29 NM_004815 181 CACGGTCTCGTGGTGAAGT 182 CAGTTGCTTGCCCAGGAC ARHGDIB NM_001175 185 TGGTCCCTAGAACAAGAGGC 186 TGATGGAGGATCAGAGGGAG ASAP2 NM_003887 189 CGGCCCATCAGCTTCTAC 190 CTCTGGCCAAAGATACAGCG ASPN NM_017680 193 TGGACTAATCTGTGGGAGCA 194 AAACACCCTTCAACACAGTCC ATM NM_000051 197 TGCTTTCTACACATGTTCAGGG 198 GTTGTGGATCGGCTCGTT ATP5E NM_006886 201 CCGCTTTCGCTACAGCAT 202 TGGGAGTATCGGATGTAGCTG ATP5J NM_ 205 GTCGACCGACTGAAACGG 206 CTCTACTTCCGGCCCTGG 001003703 ATXN1 NM_000332 209 GATCGACTCCAGCACCGTAG 210 GAACTGTATCACGGCCACG AURKA NM_003600 213 CATCTTCCAGGAGGACCACT 214 TCCGACCTTCAATCATTTCA AURKB NM_004217 217 AGCTGCAGAAGAGCTGCACAT 218 GCATCTGCCAACTCCTCCAT AXIN2 NM_004655 221 GGCTATGTCTTTGCACCAGC 222 ATCCGTCAGCGCATCACT AZGP1 NM_001185 225 GAGGCCAGCTAGGAAGCAA 226 CAGGAAGGGCAGCTACTGG BAD NM_032989 229 GGGTCAGGGGCCTCGAGAT 230 CTGCTCACTCGGCTCAAACTC BAG5 NM_ 233 ACTCCTGCAATGAACCCTGT 234 ACAAACAGCTCCCCACGA 001015049 BAK1 NM_001188 237 CCATTCCCACCATTCTACCT 238 GGGAACATAGACCCACCAAT BAX NM_004324 241 CCGCCGTGGACACAGACT 242 TTGCCGTCAGAAAACATGTCA BBC3 NM_014417 245 CCTGGAGGGTCCTGTACAAT 246 CTAATTGGGCTCCATCTCG BCL2 NM_000633 249 CAGATGGACCTAGTACCCACTGAGA 250 CCTATGATTTAAGGGCATTTTTCC BDKRB1 NM_000710 253 GTGGCAGAAATCTACCTGGC 254 GAAGGGCAAGCCCAAGAC BGN NM_001711 257 GAGCTCCGCAAGGATGAC 258 CTTGTTGTTCACCAGGACGA BIK NM_001197 261 ATTCCTATGGCTCTGCAATTGTC 262 GGCAGGAGTGAATGGCTCTTC BIN1 NM_004305 265 CCTGCAAAAGGGAACAAGAG 266 CGTGGTTGACTCTGATCTCG BIRC5 NM_ 269 TTCAGGTGGATGAGGAGACA 270 CACACAGCAGTGGCAAAAG 001012271 BMP6 NM_001718 273 GTGCAGACCTTGGTTCACCT 274 CTTAGTTGGCGCACAGCAC BMPR1B NM_001203 277 ACCACTTTGGCCATCCCT 278 GCGGTGTTTGTACCCAGTG BRCA1 NM_007294 281 TCAGGGGGCTAGAAATCTGT 282 CCATTCCAGTTGATCTGTGG BRCA2 NM_000059 285 AGTTCGTGCTTTGCAAGATG 286 AAGGTAAGCTGGGTCTGCTG BTG1 NM_001731 289 GAGGTCCGAGCGATGTGA 290 AGTTATTTTCGAGACAGGAGGC BTG3 NM_006806 293 CCATATCGCCCAATTCCA 294 CCAGTGATTCCGGTCACAA BTRC NM_033637 297 GTTGGGACACAGTTGGTCTG 298 TGAAGCAGTCAGTTGTGCTG BUB1 NM_004336 301 CCGAGGTTAATCCAGCACGTA 302 AAGACATGGCGCTCTCAGTTC C7 NM_000587 305 ATGTCTGAGTGTGAGGCGG 306 AGGCCTTATGCTGGTGACAG CACNA1D NM_000720 309 AGGACCCAGCTCCATGTG 310 CCTACATTCCGTGCCATTG CADM1 NM_014333 313 CCACCACCATCCTTACCATC 314 GATCCACTGCCCTGATCG CADPS NM_003716 317 CAGCAAGGAGACTGTGCTGA 318 GGTCCTCTTCTCCACGGTAGAT CASP3 NM_032991 325 TGAGCCTGAGCAGAGACATGA 326 CCTTCCTGCGTGGTCCAT CASP7 NM_033338 329 GCAGCGCCGAGACTTTTA 330 AGTCTCTCTCCGTCGCTCC CAV1 NM_001753 333 GTGGCTCAACATTGTGTTCC 334 CAATGGCCTCCATTTTACAG CAV2 NM_198212 337 CTTCCCTGGGACGACTTG 338 CTCCTGGTCACCCTTCTGG CCL2 NM_002982 341 CGCTCAGCCAGATGCAATC 342 GCACTGAGATCTTCCTATTGGTGAA CCL5 NM_002985 345 AGGTTCTGAGCTCTGGCTTT 346 ATGCTGACTTCCTTCCTGGT CCNB1 NM_031966 349 TTCAGGTTGTTGCAGGAGAC 350 CATCTTCTTGGGCACACAAT CCND1 NM_001758 353 GCATGTTCGTGGCCTCTAAGA 354 CGGTGTAGATGCACAGCTTCTC CCNE2 NM_057749 357 ATGCTGTGGCTCCTTCCTAACT 358 ACCCAAATTGTGATATACAAAAAGGTT CCNH NM_001239 361 GAGATCTTCGGTGGGGGTA 362 CTGCAGACGAGAACCCAAAC CCR1 NM_001295 365 TCCAAGACCCAATGGGAA 366 TCGTAGGCTTTCGTGAGGA CD164 NM_006016 369 CAACCTGTGCGAAAGTCTACC 370 ACACCCAAGACCAGGACAAT CD1A NM_001763 373 GGAGTGGAAGGAACTGGAAA 374 TCATGGGCGTATCTACGAAT CD276 NM_ 377 CCAAAGGATGCGATACACAG 378 GGATGACTTGGGAATCATGTC 001024736 CD44 NM_000610 381 GGCACCACTGCTTATGAAGG 382 GATGCTCATGGTGAATGAGG CD68 NM_001251 385 TGGTTCCCAGCCCTGTGT 386 CTCCTCCACCCTGGGTTGT CD82 NM_002231 389 GTGCAGGCTCAGGTGAAGTG 390 GACCTCAGGGCGATTCATGA CDC20 NM_001255 393 TGGATTGGAGTTCTGGGAATG 394 GCTTGCACTCCACAGGTACACA CDC25B NM_021873 397 GCTGCAGGACCAGTGAGG 398 TAGGGCAGCTGGCTTCAG CDC6 NM_001254 401 GCAACACTCCCCATTTACCTC 402 TGAGGGGGACCATTCTCTTT CDH1 NM_004360 405 TGAGTGTCCCCCGGTATCTTC 406 CAGCCGCTTTCAGATTTTCAT CDH10 NM_006727 409 TGTGGTGCAAGTCACAGCTAC 410 TGTAAATGACTCTGGCGCTG CDH11 NM_001797 413 GTCGGCAGAAGCAGGACT 414 CTACTCATGGGCGGGATG CDH19 NM_021153 417 AGTACCATAATGCGGGAACG 418 AGACTGCCTGTATAGGCTCCTG CDH5 NM_001795 421 ACAGGAGACGTGTTCGCC 422 CAGCAGTGAGGTGGTACTCTGA CDH7 NM_033646 425 GTTTGACATGGCTGCACTGA 426 AGTCACATCCCTCCGGGT CDK14 NM_012395 429 GCAAGGTAAATGGGAAGTTGG 430 GATAGCTGTGAAAGGTGTCCCT CDK2 NM_001798 433 AATGCTGCACTACGACCCTA 434 TTGGTCACATCCTGGAAGAA CDK3 NM_001258 437 CCAGGAAGGGACTGGAAGA 438 GTTGCATGAGCAGGTCCC CDK7 NM_001799 441 GTCTCGGGCAAAGCGTTAT 442 CTCTGGCCTTGTAAACGGTG CDKN1A NM_000389 445 TGGAGACTCTCAGGGTCGAAA 446 GGCGTTTGGAGTGGTAGAAATC CDKN1C NM_000076 449 CGGCGATCAAGAAGCTGT 450 CAGGCGCTGATCTCTTGC CDKN2B NM_004936 453 GACGCTGCAGAGCACCTT 454 GCGGGAATCTCTCCTCAGT CDKN2C NM_001262 457 GAGCACTGGGCAATCGTTAC 458 CAAAGGCGAACGGGAGTAG CDKN3 NM_005192 461 TGGATCTCTACCAGCAATGTG 462 ATGTCAGGAGTCCCTCCATC CDS2 NM_003818 465 GGGCTTCTTTGCTACTGTGG 466 ACAGGGCAGACAAAGCATCT CENPF NM_016343 469 CTCCCGTCAACAGCGTTC 470 GGGTGAGTCTGGCCTTCA CHAF1A NM_005483 473 GAACTCAGTGTATGAGAAGCGG 474 GCTCTGTAGCACCTGCGG CHN1 NM_001822 477 TTACGACGCTCGTGAAAGC 478 TCTCCCTGATGCACATGTCT CHRAC1 NM_017444 481 TCTCGCTGCCTCTATCCC 482 CCTGGTTGATGCTGGACA CKS2 NM_001827 485 GGCTGGACGTGGTTTTGTCT 486 CGCTGCAGAAAATGAAACGA CLDN3 NM_001306 489 ACCAACTGCGTGCAGGAC 490 GGCGAGAAGGAACAGCAC CLTC NM_004859 493 ACCGTATGGACAGCCACAG 494 TGACTACAGGATCAGCGCTTC COL11A1 NM_001854 497 GCCCAAGAGGGGAAGATG 498 GGACCTGGGTCTCCAGTTG COL1A1 NM_000088 501 GTGGCCATCCAGCTGACC 502 CAGTGGTAGGTGATGTTCTGGGA COL1A2 NM_000089 505 CAGCCAAGAACTGGTATAGGAGCT 506 AAACTGGCTGCCAGCATTG COL3A1 NM_000090 509 GGAGGTTCTGGACCTGCTG 510 ACCAGGACTGCCACGTTC COL4A1 NM_001845 513 ACAAAGGCCTCCCAGGAT 514 GAGTCCCAGGAAGACCTGCT COL5A1 NM_000093 517 CTCCCTGGGAAAGATGGC 518 CTGGACCAGGAAGCCCTC COL5A2 NM_000393 521 GGTCGAGGAACCCAAGGT 522 GCCTGGAGGTCCAACTCTG COL6A1 NM_001848 525 GGAGACCCTGGTGAAGCTG 526 TCTCCAGGGACACCAACG COL6A3 NM_004369 529 GAGAGCAAGCGAGACATTCTG 530 AACAGGGAACTGGCCCAC COL8A1 NM_001850 533 TGGTGTTCCAGGGCTTCT 534 CCCTGTAAACCCTGATCCC COL9A2 NM_001852 537 GGGAACCATCCAGGGTCT 538 ATTCCGGGTGGACAGTTG CRISP3 NM_006061 541 TCCCTTATGAACAAGGAGCAC 542 AACCATTGGTGCATAGTCCAT CSF1 NM_000757 545 TGCAGCGGCTGATTGACA 546 CAACTGTTCCTGGTCTACAAACTCA CSK NM_004383 549 CCTGAACATGAAGGAGCTGA 550 CATCACGTCTCCGAACTCC CSRP1 NM_004078 553 ACCCAAGACCCTGCCTCT 554 GCAGGGGTGGAGTGATGT CTGF NM_001901 557 GAGTTCAAGTGCCCTGACG 558 AGTTGTAATGGCAGGCACAG CTHRC1 NM_138455 561 TGGCTCACTTCGGCTAAAAT 562 TCAGCTCCATTGAATGTGAAA CTNNA1 NM_001903 565 CGTTCCGATCCTCTATACTGCAT 566 AGGTCCCTGTTGGCCTTATAGG CTNNB1 NM_001904 569 GGCTCTTGTGCGTACTGTCCTT 570 TCAGATGACGAAGAGCACAGATG CTNND1 NM_001331 573 CGGAAACTTCGGGAATGTGA 574 CTGAATCCTTCTGCCCAATCTC CTNND2 NM_001332 577 GCCCGTCCCTACAGTGAAC 578 CTCACACCCAGGAGTCGG CTSB NM_001908 581 GGCCGAGATCTACAAAAACG 582 GCAGGAAGTCCGAATACACA CTSD NM_001909 585 GTACATGATCCCCTGTGAGAAGGT 586 GGGACAGCTTGTAGCCTTTGC CTSK NM_000396 589 AGGCTTCTCTTGGTGTCCATAC 590 CCACCTCTTCACTGGTCATGT CTSL2 NM_001333 593 TGTCTCACTGAGCGAGCAGAA 594 ACCATTGCAGCCCTGATTG CTSS NM_004079 597 TGACAACGGCTTTCCAGTACAT 598 TCCATGGCTTTGTAGGGATAGG CUL1 NM_003592 601 ATGCCCTGGTAATGTCTGCAT 602 GCGACCACAAGCCTTATCAAG CXCL12 NM_000609 605 GAGCTACAGATGCCCATGC 606 TTTGAGATGCTTGACGTTGG CXCR4 NM_003467 609 TGACCGCTTCTACCCCAATG 610 AGGATAAGGCCAACCATGATGT CXCR7 NM_020311 613 CGCCTCAGAACGATGGAT 614 GTTGCATGGCCAGCTGAT CYP3A5 NM_000777 617 TCATTGCCCAGTATGGAGATG 618 GACAGGCTTGCCTTTCTCTG CYR61 NM_001554 621 TGCTCATTCTTGAGGAGCAT 622 GTGGCTGCATTAGTGTCCAT DAG1 NM_004393 625 GTGACTGGGCTCATGCCT 626 ATCCCACTTGTGCTCCTGTC DAP NM_004394 629 CCAGCCTTTCTGGTGCTG 630 GACCAGGTCTGCCTCTGC DAPK1 NM_004938 633 CGCTGACATCATGAATGTTCCT 634 TCTCTTTCAGCAACGATGTGTCTT DARC NM_002036 637 GCCCTCATTAGTCCTTGGCT 638 CAGACAGAAGGGCTGGGAC DDIT4 NM_019058 641 CCTGGCGTCTGTCCTCAC 642 CGAAGAGGAGGTGGACGA DDR2 NM_ 645 CTATTACCGGATCCAGGGC 646 CCCAGCAAGATACTCTCCCA 001014796 DES NM_001927 649 ACTTCTCACTGGCCGACG 650 GCTCCACCTTCTCGTTGGT DHRS9 NM_005771 653 GGAGAAAGGTCTCTGGGGTC 654 CAGTCAGTGGGAGCCAGC DHX9 NM_001357 657 GTTCGAACCATCTCAGCGAC 658 TCCAGTTGGATTGTGGAGGT DIAPH1 NM_005219 661 CAAGCAGTCAAGGAGAACCA 662 AGTTTTGCTCGCCTCATCTT DICER1 NM_177438 665 TCCAATTCCAGCATCACTGT 666 GGCAGTGAAGGCGATAAAGT DIO2 NM_013989 669 CTCCTTTCACGAGCCAGC 670 AGGAAGTCAGCCACTGAGGA DLC1 NM_006094 673 GATTCAGACGAGGATGAGCC 674 CACCTCTTGCTGTCCCTTTG DLGAP1 NM_004746 677 CTGCTGAGCCCAGTGGAG 678 AGCCTGGAAGGAGTTCCG DLL4 NM_019074 681 CACGGAGGTATAAGGCAGGAG 682 AGAAGGAAGGTCCAGCCG DNM3 NM_015569 685 CTTTCCCACCCGGCTTAC 686 AAGGACCTTCTGCAGGTGTG DPP4 NM_001935 689 GTCCTGGGATCGGGAAGT 690 GTACTCCCACCGGGATACAG DPT NM_001937 693 CACCTAGAAGCCTGCCCAC 694 CAGTAGCTCCCCAGGGTTC DUSP1 NM_004417 697 AGACATCAGCTCCTGGTTCA 698 GACAAACACCCTTCCTCCAG DUSP6 NM_001946 701 CATGCAGGGACTGGGATT 702 TGCTCCTACCCTATCATTTGG DVL1 NM_004421 705 TCTGTCCCACCTGCTGCT 706 TCAGACTGTTGCCGGATG DYNLL1 NM_ 709 GCCGCCTACCTCACAGAC 710 GCCTGACTCCAGCTCTCCT 001037494 EBNA1BP2 NM_006824 713 TGCGGCGAGATGGACACT 714 GTGACAAGGGATTCATCGGATT ECE1 NM_001397 717 ACCTTGGGATCTGCCTCC 718 GGACCAGGACCTCCATCTG EDN1 NM_001955 721 TGCCACCTGGACATCATTTG 722 TGGACCTAGGGCTTCCAAGTC EDNRA NM_001957 725 TTTCCTCAAATTTGCCTCAAG 726 TTACACATCCAACCAGTGCC EFNB2 NM_004093 729 TGACATTATCATCCCGCTAAGGA 730 GTAGTCCCCGCTGACCTTCTC EGF NM_001963 733 CTTTGCCTTGCTCTGTCACAGT 734 AAATACCTGACACCCTTATGACAAATT EGR1 NM_001964 737 GTCCCCGCTGCAGATCTCT 738 CTCCAGCTTAGGGTAGTTGTCCAT EGR3 NM_004430 741 CCATGTGGATGAATGAGGTG 742 TGCCTGAGAAGAGGTGAGGT EIF2C2 NM_012154 745 GCACTGTGGGCAGATGAA 746 ATGTTTGGTGACTGGCGG EIF2S3 NM_001415 749 CTGCCTCCCTGATTCAAGTG 750 GGTGGCAAGTGCCTGTAATATC EIF3H NM_003756 753 CTCATTGCAGGCCAGATAAA 754 GCCATGAAGAGCTTGCCTA EIF4E NM_001968 757 GATCTAAGATGGCGACTGTCGAA 758 TTAGATTCCGTTTTCTCCTCTTCTG EIF5 NM_001969 761 GAATTGGTCTCCAGCTGCC 762 TCCAGGTATATGGCTCCTGC ELK4 NM_001973 765 GATGTGGAGAATGGAGGGAA 766 AGTCATTGCGGCTAGAGGTC ENPP2 NM_006209 769 CTCCTGCGCACTAATACCTTC 770 TCCCTGGATAATTGGGTCTG ENY2 NM_020189 773 CCTCAAAGAGTTGCTGAGAGC 774 CCTCTTTACAGTGTGCCTTCA EPHA2 NM_004431 777 CGCCTGTTCACCAAGATTGAC 778 GTGGCGTGCCTCGAAGTC EPHA3 NM_005233 781 CAGTAGCCTCAAGCCTGACA 782 TTCGTCCCATATCCAGCG EPHB2 NM_004442 785 CAACCAGGCAGCTCCATC 786 GTAATGCTGTCCACGGTGC EPHB4 NM_004444 789 TGAACGGGGTATCCTCCTTA 790 AGGTACCTCTCGGTCAGTGG ERBB2 NM_004448 793 CGGTGTGAGAAGTGCAGCAA 794 CCTCTCGCAAGTGCTCCAT ERBB3 NM_001982 797 CGGTTATGTCATGCCAGATACAC 798 GAACTGAGACCCACTGAAGAAAGG ERBB4 NM_005235 801 TGGCTCTTAATCAGTTTCGTTACCT 802 CAAGGCATATCGATCCTCATAAAGT ERCC1 NM_001983 805 GTCCAGGTGGATGTGAAAGA 806 CGGCCAGGATACACATCTTA EREG NM_001432 809 TGCTAGGGTAAACGAAGGCA 810 TGGAGACAAGTCCTGGCAC ERG NM_004449 813 CCAACACTAGGCTCCCCA 814 CCTCCGCCAGGTCTTTAGT ESR1 NM_000125 817 CGTGGTGCCCCTCTATGAC 818 GGCTAGTGGGCGCATGTAG ESR2 NM_001437 821 TGGTCCATCGCCAGTTATCA 822 TGTTCTAGCGATCTTGCTTCACA ETV1 NM_004956 825 TCAAACAAGAGCCAGGAATG 826 AACTGCCAGAGCTGAAGTGA ETV4 NM_001986 829 TCCAGTGCCTATGACCCC 830 ACTGTCCAAGGGCACCAG EZH2 NM_004456 833 TGGAAACAGCGAAGGATACA 834 CACCGAACACTCCCTAGTCC F2R NM_001992 837 AAGGAGCAAACCATCCAGG 838 GCAGGGTTTCATTGAGCAC   FAH NM_001441 841 GACAGCGTAGTGGTGCATGT 842 AGCTGAACATGGACTGTGGA FABP5 NM_001444 845 GCTGATGGCAGAAAAACTCA 846 CTTTCCTTCCCATCCCACT FADD NM_003824 849 GTTTTCGCGAGATAACGGTC 850 CTCCGGTGCCTGATTCAC FAM107A NM_007177 853 AAGTCAGGGAAAACCTGCG 854 GCTGGCCCTACAGCTCTCT FAM13C NM_198215 857 ATCTTCAAAGCGGAGAGCG 858 GCTGGATACCACATGCTCTG FAM171B NM_177454 861 CCAGGAAGGAAAAGCACTGT 862 GTGGTCTGCCCCTTCTTTTA FAM49B NM_016623 865 AGATGCAGAAGGCATCTTGG 866 GCTGGATTGCCTCTCGTATT FAM73A NM_198549 869 TGAGAAGGTGCGCTATTCAA 870 GGCCATTAAAAGCTCAGTGC FAP NM_004460 873 GTTGGCTCACGTGGGTTAC 874 GACAGGACCGAAACATTCTG FAS NM_000043 877 GGATTGCTCAACAACCATGCT 878 GGCATTAACACTTTTGGACGATAA FASLG NM_000639 881 GCACTTTGGGATTCTTTCCATTAT 882 GCATGTAAGAAGACCCTCACTGAA FASN NM_004104 885 GCCTCTTCCTGTTCGACG 886 GCTTTGCCCGGTAGCTCT FCGR3A NM_000569 889 GTCTCCAGTGGAAGGGAAAA 890 AGGAATGCAGCTACTCACTGG FGF10 NM_004465 893 TCTTCCGTCCCTGTCACCT 894 AGAGTTGGTGGCCTCTGGT FGF17 NM_003867 897 GGTGGCTGTCCTCAAAATCT 898 TCTAGCCAGGAGGAGTTTGG FGF5 NM_004464 901 GCATCGGTTTCCATCTGC 902 AACATATTGGCTTCGTGGGA FGF6 NM_020996 905 GGGCCATTAATTCTGACCAC 906 CCCGGGACATAGTGATGAA FGF7 NM_002009 909 CCAGAGCAAATGGCTACAAA 910 TCCCCTCCTTCCATGTAATC FGFR2 NM_000141 913 GAGGGACTGTTGGCATGCA 914 GAGTGAGAATTCGATCCAAGTCTTC FGFR4 NM_002011 917 CTGGCTTAAGGATGGACAGG 918 ACGAGACTCCAGTGCTGATG FKBP5 NM_004117 921 CCCACAGTAGAGGGGTCTCA 922 GGTTCTGGCTTTCACGTCTG FLNA NM_001456 925 GAACCTGCGGTGGACACT 926 GAAGACACCCTGGCCCTC FLNC NM_001458 929 CAGGACAATGGTGATGGCT 930 TGATGGTGTACTCGCCAGG FLT1 NM_002019 933 GGCTCCTGAATCTATCTTTG 934 TCCCACAGCAATACTCCGTA FLT4 NM_002020 937 ACCAAGAAGCTGAGGACCTG 938 CCTGGAAGCTGTAGCAGACA FN1 NM_002026 941 GGAAGTGACAGACGTGAAGGT 942 ACACGGTAGCCGGTCACT FOS NM_005252 945 CGAGCCCTTTGATGACTTCCT 946 GGAGCGGGCTGTCTCAGA FOXO1 NM_002015 949 GTAAGCACCATGCCCCAC 950 GGGGCAGAGGCACTTGTA FOXP3 NM_014009 953 CTGTTTGCTGTCCGGAGG 954 GTGGAGGAACTCTGGGAATG FOXQ1 NM_033260 957 TGTTTTTGTCGCAACTTCCA 958 TGGAAAGGTTCCCTGATGTACT FSD1 NM_024333 961 AGGCCTCCTGTCCTTCTACA 962 TGTGTGAACCTGGTCTTGAAA FYN NM_002037 965 GAAGCGCAGATCATGAAGAA 966 CTCCTCAGACACCACTGCAT G6PD NM_000402 969 AATCTGCCTGTGGCCTTG 970 CGAGATGTTGCTGGTGACA GABRG2 NM_198904 973 CCACTGTCCTGACAATGACC 974 GAGATCCATCGCTGTGACAT GADD45A NM_001924 977 GTGCTGGTGACGAATCCA 978 CCCGGCAAAAACAAATAAGT GADD45B NM_015675 981 ACCCTCGACAAGACCACACT 982 TGGGAGTTCATGGGTACAGA GDF15 NM_004864 985 CGCTCCAGACCTATGATGACT 986 ACAGTGGAAGGACCAGGACT GHR NM_000163 989 CCACCTCCCACAGGTTCA 990 GGTGCGTGCCTGTAGTCC GNPTAB NM_024312 993 GGATTCACATCGCGGAAA 994 GTTCTTGCATAACAATCCGGTC GNRH1 NM_000825 997 AAGGGCTAAATCCAGGTGTG 998 CTGGATCTCTGTGGCTGGT GPM6B NM_ 1001 ATGTGCTTGGAGTGGCCT 1002 TGTAGAACATAAACACGGGCA 001001994 GPNMB NM_ 1005 CAGCCTCGCCTTTAAGGAT 1006 TGACAAATATGGCCAAGCAG 001005340 GPR68 NM_003485 1009 CAAGGACCAGATCCAGCG 1010 GGTAGGGCAGGAAGCAGG GPS1 NM_004127 1013 AGTACAAGCAGGCTGCCAAG 1014 GCAGCTCAGGGAAGTCACA GRB7 NM_005310 1017 CCATCTGCATCCATCTTGTT 1018 GGCCACCAGGGTATTATCTG GREM1 NM_013372 1021 GTGTGGGCAAGGACAAGC 1022 GACCTGATTTGGCCTCACC GSK3B NM_002093 1025 GACAAGGACGGCAGCAAG 1026 TTGTGGCCTGTCTGGACC GSN NM_000177 1029 CTTCTGCTAAGCGGTACATCGA 1030 GGCTCAAAGCCTTGCTTCAC GSTM1 NM_000561 1033 AAGCTATGAGGAAAAGAAGTACACGA 1034 GGCCCAGCTTGAATTTTTCA T GSTM2 NM_000848 1037 CTGCAGGCACTCCCTGAAAT 1038 CCAAGAAACCATGGCTGCTT HDAC1 NM_004964 1041 CAAGTACCACAGCGATGACTACATTA 1042 GCTTGCTGTACTCCGACATGTT A HDAC9 NM_178423 1045 AACCAGGCAGTCACCTTGAG 1046 CTCTGTCTTCCTGCATCGC HGD NM_000187 1049 CTCAGGTCTGCCCCTACAAT 1050 TTATTGGTGCTCCGTGGAC HIP1 NM_005338 1053 CTCAGAGCCCCACCTGAG 1054 GGGTTTCCCTGCCATACTG HIRIP3 NM_003609 1057 GGATGAGGAAAAGGGGGAT 1058 TCCCTAGCTGACTTTCTCCG HK1 NM_000188 1061 TACGCACAGAGGCAAGCA 1062 GAGAGAAGTGCTGGAGAGGC HLA-G NM_002127 1065 CCATCCCCATCATGGGTATC 1066 CCGCAGCTCCAGTGACTACA HLF NM_002126 1069 CACCCTGCAGGTGTCTGAG 1070 GGTACCTAGGAGCAGAAGGTGA HNF1B NM_000458 1073 TCCCAGCATCTCAACAAGG 1074 CGTACCAGGTGTACAGAGCG HPS1 NM_000195 1077 GCGGAAGCTGTATGTGCTC 1078 TTCGGATAAGATGACCGTCC HRAS NM_005343 1081 GGACGAATACGACCCCACT 1082 GCACGTCTCCCCATCAAT HSD17B10 NM_004493 1085 CCAGCGAGTTCTTGATGTGA 1086 ATCTCACCAGCCACCAGG HSD17B2 NM_002153 1089 GCTTTCCAAGTGGGGAATTA 1090 TGCCTGCGATATTTGTTAGG HSD17B3 NM_000197 1093 GGGACGTCCTGGAACAGT 1094 TGGAGAATCTCACGCACTTC HSD17B4 NM_000414 1097 CGGGAAGCTTCAGAGTACCTT 1098 ACCTCAGGCCCAATATCCTT HSD3B2 NM_000198 1101 GCCTTCCTTTAACCCTGATG 1102 GGAGTAAATTGGGCTGAGTAGG HSP90AB1 NM_007355 1105 GCATTGTGACCAGCACCTAC 1106 GAAGTGCCTGGGCTTTCAT HSPA5 NM_005347 1109 GGCTAGTAGAACTGGATCCCAACA 1110 GGTCTGCCCAAATGCTTTTC HSPA8 NM_006597 1113 CCTCCCTCTGGTGGTGCTT 1114 GCTACATCTACACTTGGTTGGCTTAA HSPB1 NM_001540 1117 CCGACTGGAGGAGCATAAA 1118 ATGCTGGCTGACTCTGCTC HSPB2 NM_001541 1121 CACCACTCCAGAGGTAGCAG 1122 TGGGACCAAACCATACATTG HSPE1 NM_002157 1125 GCAAGCAACAGTAGTCGCTG 1126 CCAACTTTCACGCTAACTGGT HSPG2 NM_005529 1129 GAGTACGTGTGCCGAGTGTT 1130 CTCAATGGTGACCAGGACA ICAM1 NM_000201 1133 GCAGACAGTGACCATCTACAGCTT 1134 CTTCTGAGACCTCTGGCTTCGT IER3 NM_003897 1137 GTACCTGGTGCGCGAGAG 1138 GCGTCTCCGCTGTAGTGTT IFI30 NM_006332 1141 ATCCCATGAAGCCCAGATAC 1142 GCACCATTCTTAGTGGAGCA IFIT1 NM_001548 1145 TGACAACCAAGCAAATGTGA 1146 CAGTCTGCCCATGTGGTAAT IFNG NM_000619 1149 GCTAAAACAGGGAAGCGAAA 1150 CAACCATTACTGGGATGCTC IGF1 NM_000618 1153 TCCGGAGCTGTGATCTAAGGA 1154 CGGACAGAGCGAGCTGACTT IGF1R NM_000875 1157 GCATGGTAGCCGAAGATTTCA 1158 TTTCCGGTAATAGTCTGTCTCATAGATA TC IGF2 NM_000612 1161 CCGTGCTTCCGGACAACTT 1162 TGGACTGCTTCCAGGTGTCA IGFBP2 NM_000597 1165 GTGGACAGCACCATGAACA 1166 CCTTCATACCCGACTTGAGG IGFBP3 NM_000598 1169 ACATCCCAACGCATGCTC 1170 CCACGCCCTTGTTTCAGA IGFBP5 NM_000599 1173 TGGACAAGTACGGGATGAAGCT 1174 CGAAGGTGTGGCACTGAAAGT IGKBP6 NM_002178 1177 TGAACCGCAGAGACCAACAG 1178 GTCTTGGACACCCGCAGAAT IL10 NM_000572 1181 CTGACCACGCTTTCTAGCTG 1182 CCAAGCCCAGAGACAAGATAA IL11 NM_000641 1185 TGGAAGGTTCCACAAGTCAC 1186 TCTTGACCTTGCAGCTTTGT IL17A NM_002190 1189 TCAAGCAACACTCCTAGGGC 1190 CAGCTCCTTTCTGGGTTGTG IL1A NM_000575 1193 GGTCCTTGGTAGAGGGCTACTT 1194 GGATGGAGCTTCAGGAGAGA IL1B NM_000576 1197 AGCTGAGGAAGATGCTGGTT 1198 GGAAAGAAGGTGCTCAGGTC IL2 NM_000586 1201 ACCTCAACTCCTGCCACAAT 1202 CACTGTTTGTGACAAGTGCAAG IL6 NM_000600 1205 CCTGAACCTTCCAAAGATGG 1206 ACCAGGCAAGTCTCCTCATT IL6R NM_000565 1209 CCAGCTTATCTCAGGGGTGT 1210 CTGGCGTAGAACCTTCCG IL6ST NM_002184 1213 GGCCTAATGTTCCAGATCCT 1214 AAAATTGTGCCTTGGAGGAG IL8 NM_000584 1217 AAGGAACCATCTCACTGTGTGTAAAC 1218 ATCAGGAAGGCTGCCAAGAG ILF3 NM_004516 1221 GACACGCCAAGTGGTTCC 1222 CTCAAGACCCGGATCACAA ILK NM_ 1225 CTCAGGATTTTCTCGCATCC 1226 AGGAGCAGGTGGAGACTGG 001014794 IMMT NM_006839 1229 CTGCCTATGCCAGACTCAGA 1230 GCTTTTCTGGCTTCCTCTTC ING5 NM_032329 1233 CCTACAGCAAGTGCAAGGAA 1234 CATCTCGTAGGTCTGCATGG INHBA NM_002192 1237 GTGCCCGAGCCATATAGCA 1238 CGGTAGTGGTTGATGACTGTTGA INSL4 NM_002195 1241 CTGTCATATTGCCCCATGC 1242 CAGATTCCAGCAGCCACC ITGA1 NM_181501 1245 GCTTCTTCTGGAGATGTGCTCT 1246 CCTGTAGATAATGACCTGGCCT ITGA3 NM_002204 1249 CCATGATCCTCACTCTGCTG 1250 GAAGCTTTGTAGCCGGTGAT ITGA4 NM_000885 1253 CAACGCTTCAGTGATCAATCC 1254 GTCTGGCCGGGATTCTTT ITGA5 NM_002205 1257 AGGCCAGCCCTACATTATCA 1258 GTCTTCTCCACAGTCCAGCA ITGA6 NM_000210 1261 CAGTGACAAACAGCCCTTCC 1262 GTTTAGCCTCATGGGCGTC ITGA7 NM_002206 1265 GATATGATTGGTCGCTGCTTTG 1266 AGAACTTCCATTCCCCACCAT ITGAD NM_005353 1269 GAGCCTGGTGGATCCCAT 1270 ACTGTCAGGATGCCCGTG ITGB3 NM_000212 1273 ACCGGGAGCCCTACATGAC 1274 CCTTAAGCTCTTTCACTGACTCAATCT ITGB4 NM_000213 1277 CAAGGTGCCCTCAGTGGA 1278 GCGCACACCTTCATCTCAT ITGB5 NM_002213 1281 TCGTGAAAGATGACCAGGAG 1282 GGTGAACATCATGACGCAGT ITPR1 NM_002222 1285 GAGGAGGTGTGGGTGTTCC 1286 GTAATCCCATGTCCGCGA ITPR3 NM_002224 1289 TTGCCATCGTGTCAGTGC 1290 ATGGAGCTGGCGTCATTG ITSN1 NM_003024 1293 TAACTGGGATGCATGGGC 1294 CTCTGCCTTAACTGGCCG JAG1 NM_000214 1297 TGGCTTACACTGGCAATGG 1298 GCATAGCTGTGAGATGCGG JUN NM_002228 1301 GACTGCAAAGATGGAAACGA 1302 TAGCCATAAGGTCCGCTCTC JUNB NM_002229 1305 CTGTCAGCTGCTGCTTGG 1306 AGGGGGTGTCCGTAAAGG KCNN2 NM_021614 1309 TGTGCTATTCATCCCATACCTG 1310 GGGCATAGGAGAAGGCAAG KCTD12 NM_138444 1313 AGCAGTTACTGGCAAGAGGG 1314 TGGAGACCTGAGCAGCCT KNDRBS3 NM_006558 1317 CGGGCAAGAAGAGTGGAC 1318 CTGTAGACGCCCTTTGCTGT KIAA0196 NM_014846 1321 CAGACACCAGCTCTGAGGC 1322 AACATTGTGAGGCGGACC KIAA0247 NM_014734 1325 CCGTGGGACATGGAGTGT 1326 GAAGCAAGTCCGTCTCCAAG KF4A NM_012310 1329 AGAGCTGGTCTCCTCCAAAA 1330 GCTGGTCTTGCTCTGTTTCA KIT NM_000222 1333 GAGGCAACTGCTTATGGCTTAATTA 1334 GGCACTCGGCTTGAGCAT KLC1 NM_182923 1337 AGTGGCTACGGGATGAACTG 1338 TGAGCCACAGACTGCTCACT KLF6 NM_001300 1341 CACGAGACCGGCTACTTCTC 1342 GCTCTAGGCAGGTCTGTTGC KLK1 NM_002257 1345 AACACAGCCCAGTTTGTTCA 1346 CCAGGAGGCTCATGTTGAAG KLK10 NM_002776 1349 GCCCAGAGGCTCCATCGT 1350 CAGAGGTTTGAACAGTGCAGACA KLK11 NM_006853 1353 CACCCCGGCTTCAACAAC 1354 CATCTTCACCAGCATGATGTCA KLK14 NM_022046 1357 CCCCTAAAATGTTCCTCCTG 1358 CTCATCCTCTTGGCTCTGTG KLK2 NM_005551 1361 AGTCTCGGATTGTGGGAGG 1362 TGTACACAGCCACCTGCC KLK3 NM_001648 1365 CCAAGCTTACCACCTGCAC 1366 AGGGTGAGGAAGACAACCG KLRK1 NM_007360 1369 TGAGAGCCAGGCTTCTTGTA 1370 ATCCTGGTCCTCTTTGCTGT KPNA2 NM_002266 1373 TGATGGTCCAAATGAACGAA 1374 AAGCTTCACAAGTTGGGGC KRT1 NM_006121 1377 TGGACAACAACCGCAGTC 1378 TATCCTCGTACTGGGCCTTG KRT15 NM_002275 1381 GCCTGGTTCTTCAGCAAGAC 1382 CTTGCTGGTCTGGATCATTTC KRT18 NM_000224 1385 AGAGATCGAGGCTCTCAAGG 1386 GGCCTTTTACTTCCTCTTCG KRT2 NM_000423 1389 CCAGTGACGCCTCTGTGTT 1390 GGGCATGGCTAGAAGCAC KRT5 NM_000424 1393 TCAGTGGAGAAGGAGTTGGA 1394 TGCCATATCCAGAGGAAACA KRT75 NM_004693 1397 TCAAAGTCAGGTACGAAGATGAAATT 1398 ACGTCCTTTTTCAGGGCTACAA KRT76 NM_015848 1401 ATCTCCAGACTGCTGGTTCC 1402 TCAGGGAATTAGGGGACAGA KRT8 NM_002273 1405 GGATGAAGCTTACATGAACAAGGTAG 1406 CATATAGCTGCCTGAGGAAGTTGAT A L1CAM NM_000425 1409 CTTGCTGGCCAATGCCTA 1410 TGATTGTCCGCAGTCAGG LAG3 NM_002286 1413 GCCTTAGAGCAAGGGATTCA 1414 CGGTTCTTGCTCCAGCTC LAMA3 NM_000227 1417 CCTGTCACTGAAGCCTTGG 1418 TGGGTTACTGGTCAGGACAAC LAMA4 NM_002290 1421 GATGCACTGCGGTTAGCAG 1422 CAGAGGATACGCTCAGCACC LAMA5 NM_005560 1425 CTCCTGGCCAACAGCACT 1426 ACACAAGGCCCAGCCTCT LAMB1 NM_002291 1429 CAAGGAGACTGGGAGGTGTC 1430 CGGCAGAACTGACAGTGTTC LAMB3 NM_000228 1433 ACTGACCAAGCCTGAGACCT 1434 GTCACACTTGCAGCATTTCA LAMC1 NM_002293 1437 GCCGTGATCTCAGACAGCTAC 1438 ACCTGCTTGCCCAAGAACT LAMC2 NM_005562 1441 ACTCAAGCGGAAATTGAAGCA 1442 ACTCCCTGAAGCCGAGACACT LAPTM5 NM_006762 1445 TGCTGGACTTCTGCCTGAG 1446 TGAGATAGGTGGGCACTTCC LGALS3 NM_002306 1449 AGCGGAAAATGGCAGACAAT 1450 CTTGAGGGTTTGGGTTTCCA LIG3 NM_002311 1453 GGAGGTGGAGAAGGAGCC 1454 ACAGGTGTCATCAGCGAGG LIMS1 NM_004987 1457 TGAACAGTAATGGGGAGCTG 1458 TTCTGGGAACTGCTGGAAG LOX NM_002317 1461 CCAATGGGAGAACAACGG 1462 CGCTGAGGCTGGTACTGTG LRP1 NM_002332 1465 TTTGGCCCAATGGGCTAAG 1466 GTCTCGATGCGGTCGTAGAAG LTBP2 NM_000428 1469 GCACACCCATCCTTGAGTCT 1470 GATGGCTGGCCACGTAGT LUM NM_002345 1473 GGCTCTTTTGAAGGATTGGTAA 1474 AAAAGCAGCTGAAACAGCATC MAGEA4 NM_002362 1477 GCATCTAACAGCCCTGTGC 1478 CAGAGTGAAGAATGGGCCTC MANF NM_006010 1481 CAGATGTGAAGCCTGGAGC 1482 AAGGGAATCCCCTCATGG MAOA NM_000240 1485 GTGTCAGCCAAAGCATGGA 1486 CGACTACGTCGAACATGTGG MAP3K5 NM_005923 1489 AGGACCAAGAGGCTACGGA 1490 CCTGTGGCCATTTCAATGAT MAP3K7 NM_145333 1493 CAGGCAAGAACTAGTTGCAGAA 1494 CCTGTACCAGGCGAGATGTAT MAP4K4 NM_004834 1497 TCGCCGAGATTTCCTGAG 1498 CTGTTGTCTCCGAAGAGCCT MAP7 NM_003980 1501 GAGGAACAGAGGTGTCTGCAC 1502 CTGCCAACTGGCTTTCCA MAPKAPK3 NM_004635 1505 AAGCTGCAGAGATAATGCGG 1506 GTGGGCAATGTTATGGCTG MCM2 NM_004526 1509 GACTTTTGCCCGCTACCTTTC 1510 GCCACTAACTGCTTCAGTATGAAGAG MCM3 NM_002388 1513 GGAGAACAATCCCCTTGAGA 1514 ATCTCCTGGATGGTGATGGT MCM6 NM_005915 1517 TGATGGTCCTATGTGTCACATTCA 1518 TGGGACAGGAAACACACCAA MDK NM_002391 1521 GGAGCCGACTGCAAGTACA 1522 GACTTTGGTGCCTGTGCC MDM2 NM_002392 1525 CTACAGGGACGCCATCGAA 1526 ATCCAACCAATCACCTGAATGTT MELK NM_014791 1529 AGGATCGCCTGTCAGAAGAG 1530 TGCACATAAGCAACAGCAGA MET NM_000245 1533 GACATTTCCAGTCCTGCAGTCA 1534 CTCCGATCGCACACATTTGT MGMT NM_002412 1537 GTGAAATGAAACGCACCACA 1538 GACCCTGCTCACAACCAGAC MGST1 NM_020300 1541 ACGGATCTACCACACCATTGC 1542 TCCATATCCAACAAAAAAACTCAAAG MICA NM_000247 1545 ATGGTGAATGTCACCCGC 1546 AAGCCAGAAGCCCTGCAT MKI67 NM_002417 1549 GATTGCACCAGGGCAGAA 1550 TCCAAAGTGCCTCTGCTAAGA MLXIP NM_014938 1553 TGCTTAGCTGGCATGTGG 1554 CAGCCTACTCTCCATGGGC MMP11 NM_005940 1557 CCTGGAGGCTGCAACATACC 1558 TACAATGGCTTTGGAGGATAGCA MMP2 NM_004530 1561 CAGCCAGAAGCGGAAACTTA 1562 AGACACCATCACCTGTGCC MMP7 NM_002423 1565 GGATGGTAGCAGTCTAGGGATTAACT 1566 GGAATGTCCCATACCCAAAGAA MMP9 NM_004994 1569 GAGAACCAATCTCACCGACA 1570 CACCCGAGTGTAACCATAGC MPPED2 NM_001584 1573 CCGACCAACCCTCCAATTA 1574 AGGGCATTTAGAGCTTCAGGA MRC1 NM_002438 1577 CTTGACCTCAGGACTCTGGATT 1578 GGACTGCGGTCACTCCAC MRPL13 NM_014078 1581 TCCGGTTCCCTTCGTTTAG 1582 GTGGAAAAACTGCGGAAAAC MSH2 NM_000251 1585 GATGCAGAATTGAGGCAGAC 1586 TCTTGGCAAGTCGGTTAAGA MSH3 NM_002439 1589 TGATTACCATCATGGCTCAGA 1590 CTTGTGAAAATGCCATCCAC MSH6 NM_000179 1593 TCTATTGGGGGATTGGTAGG 1594 CAAATTGCGAGTGGTGAAAT MTA1 NM_004689 1597 CCGCCCTCACCTGAAGAGA 1598 GGAATAAGTTAGCCGCGCTTCT MTPN NM_145808 1601 GGTGGAAGGAAACCTCTTCA 1602 CAGCAGCAGAAATTCCAGG MTSS1 NM_014751 1605 TTCGACAAGTCCTCCACCAT 1606 CTTGGAACATCCGTCGGTAG MUC1 NM_002456 1609 GGCCAGGATCTGTGGTGGTA 1610 CTCCACGTCGTGGACATTGA MVP NM_017458 1613 ACGAGAACGAGGGCATCTATGT 1614 GCATGTAGGTGCTTCCAATCAC MYBL2 NM_002466 1617 GCCGAGATCGCCAAGATG 1618 CTTTTGATGGTAGAGTTCCAGTGATTC MYBPC1 NM_002465 1621 CAGCAACCAGGGAGTCTGTA 1622 CAGCAGTAAGTGCCTCCATC MYC NM_002467 1625 TCCCTCCACTCGGAAGGACTA 1626 CGGTTGTTGCTGATCTGTCTCA MYLK3 NM_182493 1629 CACCTGACTGAGCTGGATGT 1630 GATGTAGTGCTGGTGCAGGT MYO6 NM_004999 1633 AAGCAGTTCTGGAGCAGGAG 1634 GATGAGCTCGGCTTCACTCT NCAM1 NM_000615 1637 TAGTTCCCAGCTGACCATCA 1638 CAGCCTTGTTCTCAGCAATG NCAPD3 NM_015261 1641 TCGTTGCTTAGACAAGGCG 1642 CTCCAGACAGTGTGCAAAGC NCOR1 NM_006311 1645 AACCGTTACAGCCCAGAATC 1646 TCTGGAGAGACCCTTGAACC NCOR2 NM_006312 1649 CGTCATCTACGAAGGCAAGA 1650 GAGCACTGGGTCACAGACAT NDRG1 NM_006096 1653 AGGGCAACATTCCACAGC 1654 CAGTGCTCCTACTCCGGC NDUFS5 NM_004552 1657 AGAAGAGTCAAGGGCACGAG 1658 AGGCCGAACCTTTTCTGG NEK2 NM_002497 1661 GTGAGGCAGCGCGACTCT 1662 TGCCAATGGTGTACAACACTTCA NETO2 NM_018092 1665 CCAGGGCACCATACTGTTTC 1666 AACGGTAAATCAAGGTCTTCGT NEXN NM_144573 1669 AGGAGGAGGAAGAAGGTAGCA 1670 GAGCTCCTGATCTGGTTTGC NFAT5 NM_006599 1673 CTGAACCCCTCTCCTGGTC 1674 AGGAAACGATGGCGAGGT NFATC2 NM_173091 1677 CAGTCAAGGTCAGAGGCTGAG 1678 CTTTGGCTCGTGGCATTC NFKB1 NM_003998 1681 CAGACCAAGGAGATGGACCT 1682 AGCTGCCAGTGCTATCCG NFKBIA NM_020529 1685 CTACTGGACGACCGCCAC 1686 CCTTGACCATCTGCTCGTACT NME1 NM_000269 1689 CCAACCCTGCAGACTCCAA 1690 ATGTATAATGTTCCTGCCAACTTGTATG NNMT NM_006169 1693 CCTAGGGCAGGGATGGAG 1694 CTAGTCCAGCCAAACATCCC NOS3 NM_000603 1697 ATCTCCGCCTCGCTCATG 1698 TCGGAGCCATACAGGATTGTC NOX4 NM_016931 1701 CCTCAACTGCAGCCTTATCC 1702 TGCTTGGAACCTTCTGTGAT NPBWR1 NM_005285 1705 TCACCAACCTGTTCATCCTC 1706 GATGTTGATGGGCAGCAC NPM1 NM_002520 1709 AATGTTGTCCAGGTTCTATTGC 1710 CAAGCAAAGGGTGGAGTTC NRG1 NM_013957 1713 CGAGACTCTCCTCATAGTGAAAGGTA 1714 CTTGGCGTGTGGAAATCTACAG T NRIP3 NM_020645 1717 CCCACAAGCATGAAGGAGA 1718 TGCTCAATCTGGCCCACTA NRP1 NM_003873 1721 CAGCTCTCTCCACGCGATTC 1722 CCCAGCAGCTCCATTCTGA NUP62 NM_153719 1725 AGCCTCTTTGCGTCAATAGC 1726 CTGTGGTCACAGGGGTACAG OAZ1 NM_004152 1729 AGCAAGGACAGCTTTGCAGT 1730 GAAGACATGGTCGGCTCG OCLN NM_002538 1733 CCCTCCCATCCGAGTTTC 1734 GACGCGGGAGTGTAGGTG ODC1 NM_002539 1737 AGAGATCACCGGCGTAATCAA 1738 CGGGCTCAGCTATGATTCTCA OLFML2B NM_015441 1741 CATGTTGGAAGGAGCGTTCT 1742 CACCAGTTTGGTGGTGACTG OLFML3 NM_020190 1745 TCAGAACTGAGGCCGACAC 1746 CCAGATAGTCTACCTCCCGCT OMD NM_005014 1749 CGCAAACTCAAGACTATCCCA 1750 CAGTCACAGCCTCAATTTCATT OR51E1 NM_152430 1753 GCATGCTTTCAGGCATTGA 1754 AGAAGATGGCCAGCATTTTG OR51E2 NM_030774 1757 TATGGTGCCAAAACCAAACA 1758 GTCCTTGTCACAGCTGATCTTG OSM NM_020530 1761 GTTTCTGAAGGGGAGGTCAC 1762 AGGTGTCTGGTTTGGGACA PAGE1 NM_003785 1765 CAACCTGACGAAGTGGAATC 1766 CAGATGCTCCCTCATCCTCT PAGE4 NM_007003 1769 GAATCTCAGCAAGAGGAACCA 1770 GTTCTTCGATCGGAGGTGTT PAK6 NM_020168 1773 CCTCCAGGTCACCCACAG 1774 GTCCCTTCAGGCCAGAACTT PATE1 NM_138294 1777 TGGTAATCCCTGGTTAACCTTC 1778 TCCACCTTATGCCTTTCACA PCA3 NR_015342 1781 CGTGATTGTCAGGAGCAAGA 1782 AGAAAGGGGAGATGCAGAGG PCDHGB7 NM_018927 1785 CCCAGCGTTGAAGCAGAT 1786 GAAACGCCAGTCCGTGTT PCNA NM_002592 1789 GAAGGTGTTGGAGGCACTCAAG 1790 GGTTTACACCGCTGGAGCTAA PDE9A NM_ 1793 TTCCACAACTTCCGGCAC 1794 AGACTGCAGAGCCAGACCA 001001570 PDGFRB NM_002609 1797 CCAGCTCTCCTTCCAGCTAC 1798 GGGTGGCTCTCACTTAGCTC PECAM1 NM_000442 1801 TGTATTTCAAGACCTCTGTGCACTT 1802 TTAGCCTGAGGAATTGCTGTGTT PEX10 NM_153818 1805 GGAGAAGTTCCCTCCCCAG 1806 ATCTGTGTCCAGGCCCAC PGD NM_002631 1809 ATTCCCATGCCCTGTTTTAC 1810 CTGGCTGGAAGCATCTCAT PGF NM_002632 1813 GTGGTTTTCCCTCGGAGC 1814 AGCAAGGGAACAGCCTCAT PGK1 NM_000291 1817 AGAGCCAGTTGCTGTAGAACTCAA 1818 CTGGGCCTACACAGTCCTTCA PGR NM_000926 1821 GATAAAGGAGCCGCGTGTCA 1822 TCACAAGTCCGGCACTTGAG PHTF2 NM_020432 1825 GATATGGCTGATGCTGCTCC 1826 GGTTTGGGTGTTCTTGTGGA PIK3C2A NM_002645 1829 ATACCAATCACCGCACAAACC 1830 CACACTAGCATTTTCTCCGCATA PIK3CA NM_006218 1833 GTGATTGAAGAGCATGCCAA 1834 GTCCTGCGTGGGAATAGC PIK3CG NM_002649 1837 GGAGAACTCAATGTCCATCTCC 1838 TGATGCTTAGGCAGGGCT PIM1 NM_002648 1841 CTGCTCAAGGACACCGTCTA 1842 GGATCCACTCTGGAGGGC PLA2G7 NM_005084 1845 CCTGGCTGTGGTTTATCCTT 1846 TGACCCATGCTGATGATTTC PLAU NM_002658 1849 GTGGATGTGCCCTGAAGGA 1850 CTGCGGATCCAGGGTAAGAA PLAUR NM_002659 1853 CCCATGGATGCTCCTCTGAA 1854 CCGGTGGCTACCAGACATTG PLG NM_000301 1857 GGCAAAATTTCCAAGACCAT 1858 ATGTATCCATGAGCGTGTGG PLK1 NM_005030 1861 AATGAATACAGTATTCCCAAGCACAT 1862 TGTCTGAAGCATCTTCTGGATGA PLOD2 NM_000935 1865 CAGGGAGGTGGTTGCAAAT 1866 TCTCCCAGGATGCATGAAG PLP2 NM_002668 1869 CCTGATCTGCTTCAGTGCC 1870 GCAGCAAGGATCATCTCAATC PNLIPRP2 NM_005396 1873 TGGAGAAGGTGAACTGCATC 1874 CACGGCTTGGGTGTACATT POSTN NM_006475 1877 GTGGCCCAATTAGGCTTG 1878 TCACAGGTGCCAGCAAAG PPAP2B NM_003713 1881 ACAAGCACCATCCCAGTGA 1882 CACGAAGAAAACTATGCAGCAG PPFIA3 NM_003660 1885 CCTGGAGCTCCGTTACTCTC 1886 AGCCACATAGGGATCCAGG PPP1R12A NM_002480 1889 CGGCAAGGGGTTGATATAGA 1890 TGCCTGGCATCTCTAAGCA PPP3CA NM_000944 1893 ATACTCCGAGCCCACGAA 1894 GGAAGCCTGTTGTTTGGC PRIMA1 NM_178013 1897 ATCCTCTTCCCTGAGCCG 1898 CCCAGCTGAGAGGGAATTTA PRKAR1B NM_002735 1901 ACAAAACCATGACTGCGCT 1902 TGTCATCCAGGTGAGCGA PRKAR2B NM_002736 1905 TGATAATCGTGGGAGTTTCG 1906 GCACCAGGAGAGGTAGCAGT PRKCA NM_002737 1909 CAAGCAATGCGTCATCAATGT 1910 GTAAATCCGCCCCCTCTTCT PRKCB NM_002738 1913 GACCCAGCTCCACTCCTG 1914 CCCATTCACGTACTCCATCA PROM1 NM_006017 1917 CTATGACAGGCATGCCACC 1918 CTCCAACCATGAGGAAGACG PROS1 NM_000313 1921 GCAGCACAGGAATCTTCTTCTT 1922 CCCACCTATCCAACCTAATCTG PSCA NM_005672 1925 ACCGTCATCAGCAAAGGCT 1926 CGTGATGTTCTTCTTGCCC PSMD13 NM_002817 1929 GGAGGAGCTCTACACGAAGAAG 1930 CGGATCCTGCACAAAATCA PTCH1 NM_000264 1933 CCACGACAAAGCCGACTAC 1934 TACTCGATGGGCTCTGCTG PTEN NM_000314 1937 TGGCTAAGTGAAGATGACAATCATG 1938 TGCACATATCATTACACCAGTTCGT PTGER3 NM_000957 1941 TAACTGGGGCAACCTTTTCT 1942 TTGCAGGAAAAGGTGACTGT PTGS2 NM_000963 1945 GAATCATTCACCAGGCAAATTG 1946 CTGTACTGCGGGTGGAACAT PTH1R NM_000316 1949 CGAGGTACAAGCTGAGATCAAGAA 1950 GCGTGCCTTTCGCTTGAA PTHLH NM_002820 1953 AGTGACTGGGAGTGGGCTAGAA 1954 AAGCCTGTTACCGTGAATCGA PTK2 NM_005607 1957 GACCGGTCGAATGATAAGGT 1958 CTGGACATCTCGATGACAGC PTK2B NM_004103 1961 CAAGCCCAGCCGACCTAAG 1962 GAACCTGGAACTGCAGCTTTG PTK6 NM_005975 1965 GTGCAGGAAAGGTTCACAAA 1966 GCACACACGATGGAGTAAGG PTK7 NM_002821 1969 TCAGAGGACTCACGGTTCG 1970 CATACACCTCCACGCTGTTG PTPN1 NM_002827 1973 AATGAGGAAGTTTCGGATGG 1974 CTTCGATCACAGCCAGGTAG PTPRK NM_002844 1977 TCAAACCCTCCCAGTGCT 1978 AGCAGCCAGTTCGTCCAG PTTG1 NM_004219 1981 GGCTACTCTGATCTATGTTGATAAGG 1982 GCTTCAGCCCATCCTTAGCA AA PYCARD NM_013258 1985 CTTTATAGACCAGCACCGGG 1986 AGCATCCAGCAGCCACTC RAB27A NM_004580 1989 TGAGAGATTAATGGGCATTGTG 1990 CCGGATGCTTTATTCGTAGG RAB30 NM_014488 1993 TAAAGGCTGAGGCACGGA 1994 CTCCCCAGCATCTCATGG RAB31 NM_006868 1997 CTGAAGGACCCTACGCTCG 1998 ATGCAAAGCCAGTGTGCTC RAD21 NM_006265 2001 TAGGGATGGTATCTGAAACAACA 2002 TCGCGTACACCTCTGCTC RAD51 NM_002875 2005 AGACTACTCGGGTCGAGGTG 2006 AGCATCCGCAGAAACCTG RAD9A NM_004584 2009 GCCATCTTCACCATCAAGG 2010 CGGTGTCTGAGAGTGTGGC RAF1 NM_002880 2013 CGTCGTATGCGAGAGTCTGT 2014 TGAAGGCGTGAGGTGTAGAA RAGE NM_014226 2017 ATTAGGGGACTTTGGCTCCT 2018 GGGTGGAGATGTATTCCGTG RALA NM_005402 2021 TGGTCCTGAATGTAGCGTGT 2022 CCCCATTTCACCTCTTCAAT RALBP1 NM_006788 2025 GGTGTCAGATATAAATGTGCAAATGC 2026 TTCGATATTGCCAGCAGCTATAAA RAP1B NM_ 2029 TGACAGCGTGAGAGGTACTAGG 2030 CTGAGCCAAGAACGACTAGCTT 001010942 RARB NM_000965 2033 ATGAACCCTTGACCCCAAGT 2034 GAGCTGGGTGAGATGCTAGG RASSF1 NM_007182 2037 AGGGCACGTGAAGTCATTG 2038 AAAGAGTGCAAACTTGCGG RB1 NM_000321 2041 CGAAGCCCTTACAAGTTTCC 2042 GGACTCTTCAGGGGTGAAAT RECK NM_021111 2045 GTCGCCGAGTGTGCTTCT 2046 GTGGGATGATGGGTTTGC REG4 NM_032044 2049 TGCTAACTCCTGCACAGCC 2050 TGCTAGGTTTCCCCTCTGAA RELA NM_021975 2053 CTGCCGGGATGGCTTCTAT 2054 CCAGGTTCTGGAAACTGTGGAT RFX1 NM_002918 2057 TCCTCTCCAAGTTCGAGCC 2058 CAGGCCCTGGTACAGCAC RGS10 NM_ 2061 AGACATCCACGACAGCGAT 2062 CCATTTGGCTGTGCTCTTG 001005339 RGS7 NM_002924 2065 CAGGCTGCAGAGAGCATTT 2066 TTTGCTTGTGCTTCTGCTTG RHOA NM_001664 2069 TGGCATAGCTCTGGGGTG 2070 TGCCACAGCTGCATGAAC RHOB NM_004040 2073 AAGCATGAACAGGACTTGACC 2074 CCTCCCCAAGTCAGTTGC RHOC NM_175744 2077 CCCGTTCGGTCTGAGGAA 2078 GAGCACTCAAGGTAGCCAAAGG RLN1 NM_006911 2081 AGCTGAAGGCAGCCCTATC 2082 TTGGAATCCTTTAATGCAGGT RND3 NM_005168 2085 TCGGAATTGGACTTGGGAG 2086 CTGGTTACTCCCCTCCAACA RNF114 NM_018683 2089 TGACAGGGGAAGTGGGTC 2090 GGAAGACAGCTTTGGCAAGA ROBO2 NM_002942 2093 CTACAAGGCCCAGCCAAC 2094 CACCAGTGGCTTTACATTTCAG RRM1 NM_001033 2097 GGGCTACTGGCAGCTACATT 2098 CTCTCAGCATCGGTACAAGG RRM2 NM_001034 2101 CAGCGGGATTAAACAGTCCT 2102 ATCTGCGTTGAAGCAGTGAG S100P NM_005980 2105 AGACAAGGATGCCGTGGATAA 2106 GAAGTCCACCTGGGCATCTC SAT1 NM_002970 2109 CCTTTTACCACTGCCTGGTT 2110 ACAATGCTGTGTCCTTCCG SCUBE2 NM_020974 2113 TGACAATCAGCACACCTGCAT 2114 TGTGACTACAGCCGTGATCCTTA SDC1 NM_002997 2117 GAAATTGACGAGGGGTGTCT 2118 AGGAGCTAACGGAGAACCTG SDC2 NM_002998 2121 GGATTGAAGTGGCTGGAAAG 2122 ACCAGCCACAGTACCCTCA SDHC NM_003001 2125 CTTCCCTCGGGTCTCAGG 2126 TTCCCTCCTGGTAAAGGTCA SEC14L1 NM_ 2129 AGGGTTCCCATGTGACCAG 2130 GCAGGCATGCTGTGGAAT 001039573 SEC23A NM_006364 2133 CGTGTGCATTAGATCAGACAGG 2134 CCCATTACCATGTATCCTCCAG SEMA3A NM_006080 2137 TTGGAATGCAGTCCGAAGT 2138 CTCTTCATTTCGCCTCTGGA SEPT9 NM_006640 2141 CAGTGACCACGAGTACCAGG 2142 CTTCGATGGTACCCCACTTG SERPINA3 NM_001085 2145 GTGTGGCCCTGTCTGCTTA 2146 CCCTGTGCATGTGAGAGCTAC SERPINB5 NM_002639 2149 CAGATGGCCACTTTGAGAACATT 2150 GGCAGCATTAACCACAAGGATT SESN3 NM_144665 2153 GACCCTGGTTTTGGGTATGA 2154 GAGCTCGGAATGTTGGCA SFRP4 NM_003014 2157 TACAGGATGAGGCTGGGC 2158 GTTGTTAGGGCAAGGGGC SH3RF2 NM_152550 2161 CCATCACAACAGCCTTGAAC 2162 CACTGGGGTGCTGATCTCTA SH3YL1 NM_015677 2165 CCTCCAAAGCCATTGTCAAG 2166 CTTTGAGAGCCAGAGTTCAGC SHH NM_000193 2169 GTCCAAGGCACATATCCACTG 2170 GAAGCAGCCTCCCGATTT SHMT2 NM_005412 2173 AGCGGGTGCTAGAGCTTGTA 2174 ATGGCACTTCGGTCTCCA SIM2 NM_005069 2177 GATGGTAGGAAGGGATGTGC 2178 CACAAGGAGCTGTGAATGAGG SIPA1L1 NM_015556 2181 CTAGGACAGCTTGGCTTCCA 2182 CATAACCGTAGGGCTCCACA SKIL NM_005414 2185 AGAGGCTGAATATGCAGGACA 2186 CTATCGGCCTCAGCATGG SLC22A3 NM_021977 2189 ATCGTCAGCGAGTTTGACCT 2190 CAGGATGGCTTGGGTGAG SLC25A21 NM_030631 2193 AAGTGTTTTTCCCCCTTGAGAT 2194 GGCCGATCGATAGTCTCTCTT SLC44A1 NM_080546 2197 AGGACCGTAGCTGCACAGAC 2198 ATCCCATCCCAATGCAGA SMAD4 NM_005359 2201 GGACATTACTGGCCTGTTCACA 2202 ACCAATACTCAGGAGCAGGATGA SMARCC2 NM_003075 2205 TACCGACTGAACCCCCAA 2206 GACATCACCCGCTAGGTTTC SMARCD1 NM_003076 2209 CCGAGTTAGCATATCCCAGG 2210 CCTTTGTGCCCAGCTGTC SMO NM_005631 2213 GGCATCCAGTGCCAGAAC 2214 CGCGATGTAGCTGTGCAT SNAI1 NM_005985 2217 CCCAATCGGAAGCCTAACTA 2218 GTAGGGCTGCTGGAAGGTAA SNRPB2 NM_003092 2221 CGTTTCCTGCTTTTGGTTCT 2222 AGGTAGAAGGCGCACGAA SOD1 NM_000454 2225 TGAAGAGAGGCATGTTGGAG 2226 AATAGACACATCGGCCACAC SORBS1 NM_015385 2229 GCAGATGAGTGGAGGCTTTC 2230 AGCGAGTGAAGAGGGCTG SOX4 NM_003107 2233 AGATGATCTCGGGAGACTGG 2234 GCGCCCTTCAGTAGGTGA SPARC NM_003118 2237 TCTTCCCTGTACACTGGCAGTTC 2238 AGCTCGGTGTGGGAGAGGTA SPARCL1 NM_004684 2241 GGCACAGTGCAAGTGATGA 2242 GATTGAGCTCTCTCGGCCT SPDEF NM_012391 2245 CCATCCGCCAGTATTACAAG 2246 GGGTGCACGAACTGGTAGA SPINK1 NM_003122 2249 CTGCCATATGACCCTTCCAG 2250 GTTGAAAACTGCACCGCAC SPINT1 NM_003710 2253 ATTCCCAGCACAGGCTCTGT 2254 AGATGGCTACCACCACCACAA SPP1 NM_ 2257 TCACACATGGAAAGCGAGG 2258 GTTCAGGTCCTGGGCAAC 001040058 SQLE NM_003129 2261 ATTTTCGAGGCCAAAAAATC 2262 CCTGAGCAAGGATATTCACG SRC NM_005417 2265 TGAGGAGTGGTATTTTGGCAAGA 2266 CTCTCGGGTTCTCTGCATTGA SRD5A1 NM_001047 2269 GGGCTGGAATCTGTCTAGGA 2270 CCATGACTGCACAATGGCT SRD5A2 NM_000348 2273 GTAGGTCTCCTGGCGTTCTG 2274 TCCCTGGAAGGGTAGGAGTAA STS NM_005418 2277 CCTGTCCTGCCAGAGCAT 2278 CAGCTGCACAAAACTGGC STAT1 NM_007315 2281 GGGCTCAGCTTTCAGAAGTG 2282 ACATGTTCAGCTGGTCCACA STAT3 NM_003150 2285 TCACATGCCACTTTGGTGTT 2286 CTTGCAGGAAGCGGCTATAC STAT5A NM_003152 2289 GAGGCGCTCAACATGAAATTC 2290 GCCAGGAACACGAGGTTCTC STAT5B NM_012448 2293 CCAGTGGTGGTGATCGTTCA 2294 GCAAAAGCATTGTCCCAGAGA STMN1 NM_005563 2297 AATACCCAACGCACAAATGA 2298 GGAGACAATGCAAACCACAC STS NM_000351 2301 GAAGATCCCTTTCCTCCTACTGTTC 2302 GGATGATGTTCGGCCTTGAT SULF1 NM_015170 2305 TGCAGTTGTAGGGAGTCTGG 2306 TCTCAAGAATTGCCGTTGAC SUMO1 NM_003352 2309 GTGAAGCCACCGTCATCATG 2310 CCTTCCTTCTTATCCCCCAAGT SVIL NM_003174 2313 ACTTGCCCAGCACAAGGA 2314 GACACCATCCGTGTCACATC TAF2 NM_003184 2317 GCGCTCCACTCTCAGTCTTT 2318 CTTGTGCTCATGGTGATGGT TARP NM_ 2321 GAGCAACACGATTCTGGGA 2322 GGCACCGTTAACCAGCTAAAT 001003799 TBP NM_003194 2325 GCCCGAAACGCCGAATATA 2326 CGTGGCTCTCTTATCCTCATGAT TFDP1 NM_007111 2329 TGCGAAGTGCTTTTGTTTGT 2330 GCCTTCCAGACAGTCTCCAT TFF1 NM_003225 2333 GCCCTCCCAGTGTGCAAAT 2334 CGTCGATGGTATTAGGATAGAAGCA TFF3 NM_003226 2337 AGGCACTGTTCATCTCAGTTTTTCT 2338 CATCAGGCTCCAGATATGAACTTTC TGFA NM_003236 2341 GGTGTGCCACAGACCTTCCT 2342 ACGGAGTTCTTGACAGAGTTTTGA TGFB1I1 NM_ 2345 GCTACTTTGAGCGCTTCTCG 2346 GGTCACCATCTTGTGTCGG 001042454 TGFB2 NM_003238 2349 ACCAGTCCCCCAGAAGACTA 2350 CCTGGTGCTGTTGTAGATGG TGFB3 NM_003239 2353 GGATCGAGCTCTTCCAGATCCT 2354 GCCACCGATATAGCGCTGTT TGFBR2 NM_003242 2357 AACACCAATGGGTTCCATCT 2358 CCTCTTCATCAGGCCAAACT THBS2 NM_003247 2361 CAAGACTGGCTACATCAGAGTCTTAG 2362 CAGCGTAGGTTTGGTCATAGATAGG TG THY1 NM_006288 2365 GGACAAGACCCTCTCAGGCT 2366 TTGGAGGCTGTGGGTCAG TIAM1 NM_003253 2369 GTCCCTGGCTGAAAATGG 2370 GGGCTCCCGAAGTCTTCTA TIMP2 NM_003255 2373 TCACCCTCTGTGACTTCATCGT 2374 TGTGGTTCAGGCTCTTCTTCTG TIMP3 NM_000362 2377 CTACCTGCCTTGCTTTGTGA 2378 ACCGAAATTGGAGAGCATGT TK1 NM_003258 2381 GCCGGGAAGACCGTAATTGT 2382 CAGCGGCACCAGGTTCAG TMPRSS2 NM_005656 2385 GGACAGTGTGCACCTCAAAG 2386 CTCCCACGAGGAAGGTCC TMPRSS2 0Q204772 2389 GAGGCGGAGGGCGAG 2390 ACTGGTCCTCACTCACAACT ERGA TMPRSS2 0Q204773 2393 GAGGCGGAGGGCGAG 2394 TTCCTCGGGTCTCCAAAGAT ERGB TNF NM_000594 2397 GGAGAAGGGTGACCGACTCA 2398 TGCCCAGACTCGGCAAAG TNFRSF10A NM_003844 2401 TGCACAGAGGGTGTGGGTTAC 2402 TCTTCATCTGATTTACAAGCTGTACATG TNFRSF10B NM_003842 2405 CTCTGAGACAGTGCTTCGATGACT 2406 CCATGAGGCCCAACTTCCT TNFRSF18 NM_148901 2409 CAGAAGCTGCCAGTTCCC 2410 CACCCACAGGTCTCCCAG TNFSF10 NM_003810 2413 CTTCACAGTGCTCCTGCAGTCT 2414 CATCTGCTTCAGCTCGTTGGT TNFSF11 NM_003701 2417 AACTGCATGTGGGCTATGG 2418 TGACACCCTCTCCACTTCAG TOP2A NM_001067 2421 AATCCAAGGGGGAGAGTGAT 2422 GTACAGATTTTGCCCGAGGA TP53 NM_000546 2425 CTTTGAACCCTTGCTTGCAA 2426 CCCGGGACAAAGCAAATG TP63 NM_003722 2429 CCCCAAGCAGTGCCTCTACA 2430 GAATCGCACAGCATCAATAACAC TPD52 NM_005079 2433 GCCTGTGAGATTCCTACCTTTG 2434 ATGTGCTTGGACCTCGCTT TPM1 NM_ 2437 TCTCTGAGCTCTGCATTTGTC 2438 GGCTCTAAGGCAGGATGCTA 001018005 TPM2 NM_213674 2441 AGGAGATGCAGCTGAAGGAG 2442 CCACCTCTTCATATTTGCGG TPP2 NM_003291 2445 TAACCGTGGCATCTACCTCC 2446 ATGCCAACGCCATGATCT TPX2 NM_012112 2449 TCAGCTGTGAGCTGCGGATA 2450 ACGGTCCTAGGTTTGAGGTTAAGA TRA2A NM_013293 2453 GCAAATCCAGATCCCAACAC 2454 CTTCACGAAGATCCCTCTCTG TRAF3IP2 NM_147200 2457 CCTCACAGGAACCGAGCA 2458 CTGGGGCTGGGAATCATA TRAM1 NM_014294 2461 CAAGAAAAGCACCAAGAGCC 2462 ATGTCCGCGTGATTCTGC TRAP1 NM_016292 2465 TTACCAGTGGCTTTCAGATGG 2466 TGTCCCGGTTCTAACTCCC TRIM14 NM_033220 2469 CATTCGCCTTAAGGAAAGCA 2470 CAAGGTACCTGGCTTGGTG TRO NM_177556 2473 GCAACTGCCACCCATACAG 2474 TGGTGTGGATACTGGCTGTC TRPC6 NM_004621 2477 CGAGAGCCAGGACTATCTGC 2478 TAGCCGTAGCAAGGCAGC TRPV6 NM_018646 2481 CCGTAGTCCCTGCAACCTC 2482 TCCTCACTGTTCACACAGGC TSTA3 NM_003313 2485 CAATTTGGACTTCTGGAGGAA 2486 CACCTCAAAGGCCGAGTG TUBB2A NM_001069 2489 CGAGGACGAGGCTTAAAAAC 2490 ACCATGCTTGAGGACAACAG TYMP NM_001953 2493 CTATATGCAGCCAGAGATGTGACA 2494 CCACGAGTTTCTTACTGAGAATGG TYMS NM_001071 2497 GCCTCGGTGTGCCTTTCA 2498 CGTGATGTGCGCAATCATG UAP1 NM_003115 2501 CTGGAGACGGTCGTAGCTG 2502 GCCAAGCTTTGTAGAAATAGGG UBE2C NM_007019 2505 TGTCTGGCGATAAAGGGATT 2506 ATGGTCCCTACCCATTTGAA UBE2G1 NM_003342 2509 TGACACTGAACGAGGTGGC 2510 AAGCAGAGAGGAATCGCCT UBE2T NM_014176 2513 TGTTCTCAAATTGCCACCAA 2514 AGAGGTCAACACAGTTGCGA UGDH NM_003359 2517 GAAACTCCAGAGGGCCAGA 2518 CTCTGGGAACCCAGTGCTC UGT2B15 NM_001076 2521 AAGCCTGAAGTGGAATGACTG 2522 CCTCCATTTAAAACCCTCCA UGT2B17 NM_001077 2525 TTGAGTTTGTCATGCGCC 2526 TCCAGGTGAGGTTGTGGG UHRF1 NM_013282 2529 CTACAGGGGCAAACAGATGG 2530 GGTGTCATTCAGGCGGAC UTP23 NM_032334 2533 GATTGCACAAAAATGCCAAG 2534 GGAAAGCAGACATTCTGATCC VCAM1 NM_001078 2537 TGGCTTCAGGAGCTGAATACC 2538 TGCTGTCGTGATGAGAAAATAGTG VCL NM_003373 2541 GATACCACAACTCCCATCAAGCT 2542 TCCCTGTTAGGCGCATCAG VCPIP1 NM_025054 2545 TTTCTCCCAGTACCATTCGTG 2546 TGAATAGGGAGCCTTGGTAGG VDR NM_000376 2549 CCTCTCCTTCCAGCCTGAGT 2550 TCATTGCCAAACACTTCGAG VEGFA NM_003376 2553 CTGCTGTCTTGGGTGCATTG 2554 GCAGCCTGGGACCACTTG VEGFB NM_003377 2557 TGACGATGGCCTGGAGTGT 2558 GGTACCGGATCATGAGGATCTG VEGFC NM_005429 2561 CCTCAGCAAGACGTTATTTGAAATT 2562 AAGTGTGATTGGCAAAACTGATTG VIM NM_003380 2565 TGCCCTTAAAGGAACCAATGA 2566 GCTTCAACGGCAAAGTTCTCTT VTI1B NM_006370 2569 ACGTTATGCACCCCTGTCTT 2570 CCGATGGAGTTTAGCAAGGT WDR19 NM_025132 2573 GAGTGGCCCAGATGTCCATA 2574 GATGCTTGAGGGCTTGGTT WFDC1 NM_021197 2577 ACCCCTGCTCTGTCCCTC 2578 ATACCTTCGGCCACGTCAC WISP1 NM_003882 2581 AGAGGCATCCATGAACTTCACA 2582 CAAACTCCACAGTACTTGGGTTGA WNT5A NM_003392 2585 GTATCAGGACCACATGCAGTACATC 2586 TGTCGGAATTGATACTGGCATT WWOX NM_016373 2589 ATCGCAGCTGGTGGGTGTAC 2590 AGCTCCCTGTTGCATGGACTT XIAP NM_001167 2593 GCAGTTGGAAGACACAGGAAAGT 2594 TGCGTGGCACTATTTTCAAGA XRCC5 NM_021141 2597 AGCCCACTTCAGCGTCTC 2598 AGCAGGATTCACACTTCCAAC YY1 NM_003403 2601 ACCCGGGCAACAAGAAGT 2602 GACCGAGAACTCGCCCTC ZFHX3 NM_006885 2605 CTGTGGAGCCTCTGCCTG 2606 GGAGCAGGGTTGGATTGAG ZFP36 NM_003407 2609 CATTAACCCACTCCCCTGA 2610 CCCCCACCATCATGAATACT ZMYND8 NM_183047 2613 GGTCTGGGCCAAACTGAAG 2614 TGCCCGTCTTTATCCCTTAG ZNF3 NM_017715 2617 CGAAGGGACTCTGCTCCA 2618 GCAGGAGGTCCTCAGAAGG ZNF827 NM_178835 2621 TGCCTGAGGACCCTCTACC 2622 GAGGTGGCGGAGTGACTTT ZWINT NM_007057 2625 TAGAGGCCATCAAAATTGGC 2626 TCCGTTTCCTCTGGGCTT SEQ SEQ Official ID ID Symbol: NO Probe Sequence: NO Amplicon Sequence: AAMP 3 CGCTTCAAAGGACCAGACCTCCTC 4 GTGTGGCAGGTGGACACTAAGGAGGAGGTCTGGTCCTTTGAA GCGGGAGACCTGGAGTGGATGGAG ABCA5 7 CACATGTGGCGAGCAATTCGAACT 5 GGTATGGATCCCAAAGCCAAACAGCACATGTGGCGAGCAATT CGAACTGCATTTAAAAACAGAAAGCGGGCTG ABCB1 11 CAAGCCTGGAACCTATAGCC 12 AAACACCACTGGAGCATTGACTACCAGGCTCGCCAATGATGCT GCTCAAGTTAAAGGGGCTATAGGTTCCAGGCTTG ABCC1 15 ACCTGATACGTCTTGGTCTTCATCGCC 16 TCATGGTGCCCGTCAATGCTGTGATGGCGATGAAGACCAAGA AT CGTATCAGGTGGCCCACATGAAGAGCAAAGACAATCG ABCC3 19 TCTGTCCTGGCTGGAGTCGCTTTCAT 20 TCATCCTGGCGATCTACTTCCTCTGGCAGAACCTAGGTCCCTC TGTCCTGGCTGGAGTCGCTTTCATGGTCTTGCTGATTCCACTC AACGG ABCC4 23 CGGAGTCCAGTGTTTTCCCACTTA 24 AGCGCCTGGAATCTACAACTCGGAGTCCAGTGTTTTCCCACTT ATCATCTTCTCTCCAGGGGCTCT ABCC8 27 AGTCTCTTGGCCACCTTCAGCCCT 28 CGTCTGTCACTGTGGAGTGGACAGGGCTGAAGGTGGCCAAGA GACTGCACCGCAGCCTGCTAAACCGGATCA ABCG2 31 ACGAAGATTTGCCTCCACCTGTGG 32 GGTCTCAACGCCATCCTGGGACCCACAGGTGGAGGCAAATCT TCGTTATTAGATGTCTTAGCTGCAAGGAAAGATCCAAG ABHD2 35 CAGGTGGCTCCTTTGATCCCTGA 36 GTAGTGGGTCTGCATGGATGTTTCAGGGATCAAAGGAGCCAC CTGGGCGCCTGAGTGCCAACCCTCA ACE 39 TGCCCTCAGCAATGAAGCCTACAA 40 CCGCTGTACGAGGATTTCACTGCCCTCAGCAATGAAGCCTACA AGCAGGACGGCTTCACAGACACGG ACOX2 43 TGCTCTCAACTTTCCTGCGGAGTG 44 ATGGAGGTGCCCAGAACACTGCACTCCGCAGGAAAGTTGAGA GCATCATCCACAGTTACCCGGAGT ACTR2 47 CCCGCAGAAAGCACATGGTATTCC 48 ATCCGCATTGAAGACCCACCCCGCAGAAAGCACATGGTATTCC TGGGTGGTGCAGTTCTAGCGGAT ADAM15 51 TCAGCCACAATCACCAACTCCACA 52 GGCGGGATGTGGTAACAGAGACCAAGACTGTGGAGTTGGTGA TTGTGGCTGATCACTCGGAGGCCCAGAAAT ADAMTS1 55 CAAGCCAAAGGCATTGGCTACTTCTTCG 56 GGACAGGTGCAAGCTCATCTGCCAAGCCAAAGGCATTGGCTA CTTCTTCGTTTTGCAGCCCAAGGTTGTAGAT ADH5 59 TGTCTGCCCATTATCTTCATTCTGCAA 60 ATGCTGTCATCATTGTCACGGTTTGTCTGCCCATTATCTTCATT CTGCAAGGGAAAGGGAAAGGAAGCAG AFAP1 63 CCTCCAGTGCTGTGTTCCCAGAAG 64 GATGTCCATCCTTGAAACAGCCTCTTCTGGGAACACAGCACTG GAGGTCTCCAGGCATCAGGGTTG AGTR1 67 ATTGTTCACCCAATGAAGTCCCGC 68 AGCATTGATCGATACCTGGCTATTGTTCACCCAATGAAGTCCC GCCTTCGACGCACAATGCTTGTAG AGTR2 71 CCACCCAGACCCCATGTAGCAAAA 72 ACTGGCATAGGAAATGGTATCCAGAATGGAATTTTGCTACATG GGGTCTGGGTGGGGGCAAAGAGACCCAGTCAAT AIG1 75 AATCGAGATGAGGACATCGCACCA 76 CGACGGTTCTGCCCTTTATATTAATCGAGATGAGGACATCGCA CCATCAGTATCCCAGCAGGAGCA AKAP1 79 CTCCACCAGGGACCGGTTTATCAA 80 TGTGGTTGGAGATGAAGTGGTGTTGATAAACCGGTCCCTGGTG GAGCGAGGCCTTGCCCAGTGGGTAGAC AKR1C1 83 CCAAATCCCAGGACAGGCATGAAG 84 GTGTGTGAAGCTGAATGATGGTCACTTCATGCCTGTCCTGGGA TTTGGCACCTATGCGCCTGCAGAG AKR1C3 87 TGCGTCACCATCCACACACAGGG 88 GCTTTGCCTGATGTCTACCAGAAGCCCTGTGTGTGGATGGTGA CGCAGAGGACGTCTCTATGCCGGTGACTGGAC AKT1 91 CAGCCCTGGACTACCTGCACTCGG 92 CGCTTCTATGGCGCTGAGATTGTGTCAGCCCTGGACTACCTGC ACTCGGAGAAGAACGTGGTGTACCGGGA AKT2 95 CAGGTCACGTCCGAGGTCGACACA 96 TCCTGCCACCCTTCAAACCTCAGGTCACGTCCGAGGTCGACA CAAGGTACTTCGATGATGAATTTACCGCC AKT3 99 TCACGGTACACAATCTTTCCGGA 100 TTGTCTCTGCCTTGGACTATCTACATTCCGGAAAGATTGTGTAC CGTGATCTCAAGTTGGAGAATCTAATGCTGG ALCAM 103 CCAGTTCCTGCCGTCTGCTCTTCT 104 GAGGAATATGGAATCCAAGGGGGCCAGTTCCTGCCGTCTGCT CTTCTGCCTCTTGATCTCCGCCAC ALDH18A1 107 CCTGAAACTTGCATCTCCTGCTGC 108 GATGCAGCTGGAACCCAAGCTGCAGCAGGAGATGCAAGTTTC AGGATGTTCCCCACTGAGCTGGAG ALDH1A2 111 TCTCTGTAGGGCCCAGCTCTCAGG 112 CACGTCTGTCCCTCTCTGCTTTCTCTGTAGGGCCCAGCTCTCA GGAATACAAAGTTGAGCCACGGTC ALKBH3 115 TAAACAGGGCAGTCACTTTCCGCA 116 TCGCTTAGTCTGCACCTCAACCGTGCGGAAAGTGACTGCCCTG TTTACTGAGGAAAAACTGGGGCTCAGA ALOX12 119 CATGCTGTTGAGACGCTCGACCTC 120 AGTTCCTCAATGGTGCCAACCCCATGCTGTTGAGACGCTCGAC CTCTCTGCCCTCCAGGCTAGTGCT ALOX5 123 CCGCATGCCGTACACGTAGACATC 124 GAGCTGCAGGACTTCGTGAACGATGTCTACGTGTACGGCATG CGGGGCCGCAAGTCCTCAGGCTTC AMACR 127 TCCATGTGTTTGATTTCTCCTCAGGC 128 GTCTCTGGGCTGTCAGCTTTCCTTTCTCCATGTGTTTGATTTCT CCTCAGGCTGGTAGCAAGTTCTGGATCTTATACCCA AMPD3 131 TACTCTCCCAACATGCGCTGGATC 132 TGGTTCATCCAGCACAAGGTCTACTCTCCCAACATGCGCTGGA TCATCCAGGTGCCCCGGATTTATG ANGPT2 135 AAGCTGACACAGCCCTCCCAAGTG 136 CCGTGAAAGCTGCTCTGTAAAAGCTGACACAGCCCTCCCAAGT GAGCAGGACTGTTCTTCCCACTGCAA ANLN 139 CCAAAGAACTCGTGTCCCTCGAGC 140 TGAAAGTCCAAAACCAGGAAAATTCCAAAGAACTCGTGTCCCT CGAGCTGAATCTGGTGATAGCCTTGGTTCTG ANPEP 143 CTCCCCAACACGCTGAAACCCG 144 CCACCTTGGACCAAAGTAAAGCGTGGAATCGTTACCGCCTCCC CAACACGCTGAAACCCGATTCCTACCGGGTGACGCTGAGA ANXA2 147 CCACCACACAGGTACAGCAGCGCT 148 CAAGACACTAAGGGCGACTACCAGAAAGCGCTGCTGTACCTG TGTGGTGGAGATGACTGAAGCCCGACACG APC 151 CATTGGCTCCCCGTGACCTGTA 152 GGACAGCAGGAATGTGTTTCTCCATACAGGTCACGGGGAGCC AATGGTTCAGAAACAAATCGAGTGGGT APEX1 155 CTTTCGGGAAGCCAGGCCCTT 156 GATGAAGCCTTTCGCAAGTTCCTGAAGGGCCTGGCTTCCCGAA AGCCCCTTGTGCTGTGTGGAGACCT APOC1 159 AGGACAGGACCTCCCAACCAAGC 160 CCAGCCTGATAAAGGTCCTGCGGGCAGGACAGGACCTCCCAA CCAAGCCCTCCAGCAAGGATTCAGAGTG APOE 163 ACTGGCGCTGCATGTCTTCCAC 164 GCCTCAAGAGCTGGTTCGAGCCCCTGGTGGAAGACATGCAGC GCCAGTGGGCCGGGCTGGTGGAGAAGGTGCAGG APRT 167 CCTTAAGCGAGGTCAGCTCCACCA 168 GAGGTCCTGGAGTGCGTGAGCCTGGTGGAGCTGACCTCGCTT AAGGGCAGGGAGAAGCTGGCACCT AQP2 171 CTCCTTCCCTTCCCCTTCTCCTGA 172 GTGTGGGTGCCAGTCCTCCTCAGGAGAAGGGGAAGGGAAGG AGGCCACTTTGAGAGGGCTGAAGGG AR 175 ACCATGCCGCCAGGGTACCACA 176 CGACTTCACCGCACCTGATGTGTGGTACCCTGGCGGCATGGT GAGCAGAGTGCCCTATCCCAGTCCCACTTGTGTCA ARF1 179 CTTGTCCTTGGGTCACCCTGCA 180 CAGTAGAGATCCCCGCAACTCGCTTGTCCTTGGGTCACCCTGC ATTCCATAGCCATGTGCTTGT ARHGAP29 183 ATGCCAGACCCAGACAAAGCATCA 184 CACGGTCTCGTGGTGAAGTCAATGCCAGACCCAGACAAAGCA TCAGCTTGTCCTGGGCAAGCAACTG ARHGDIB 187 TAAAACCGGGCTTTCACCCAACCT 188 TGGTCCCTAGAACAAGAGGCTTAAAACCGGGCTTTCACCCAAC CTGCTCCCTCTGATCCTCCATCA ASAP2 191 CTGGGCTCCAACCAGCTTCAGTCT 192 CGGCCCATCAGCTTCTACCAGCTGGGCTCCAACCAGCTTCAG TCTAACGCTGTATCTTTGGCCAGAG ASPN 195 AGTATCACCCAGGGTGCAGCCAC 196 TGGACTAATCTGTGGGAGCAGTTTATTCCAGTATCACCCAGGG TGCAGCCACACCAGGACTGTGTTGAAGGGTGTTT ATM 199 CCAGCTGTCTTCGACACTTCTCGC 200 TGCTTTCTACACATGTTCAGGGATTTTTCACCAGCTGTCTTCGA CACTTCTCGCAAACGAGCCGATCCACAAC ATP5E 203 TCCAGCCTGTCTCCAGTAGGCCAC 204 CCGCTTTCGCTACAGCATGGTGGCCTACTGGAGACAGGCTGG ACTCAGCTACATCCGATACTCCCA ATP5J 207 CTACCCGCCATCGCAATGCATTAT 208 GTCGACCGACTGAAACGGCGGCCCATAATGCATTGCGATGGC GGGTAGGCGTGTGGGGGCGGAGCCAGGGCCGGAAGTAGAG ATXN1 211 CGGGCTATGGCTGTCTTCAATCCT 212 GATCGACTCCAGCACCGTAGAGAGGATTGAAGACAGCCATAG CCCGGGCGTGGCCGTGATACAGTTC AURKA 215 CTCTGTGGCACCCTGGACTACCTG 216 CATCTTCCAGGAGGACCACTCTCTGTGGCACCCTGGACTACCT GCCCCCTGAAATGATTGAAGGTCGGA AURKB 219 TGACGAGCAGCGAACAGCCACG 220 AGCTGCAGAAGAGCTGCACATTTGACGAGCAGCGAACAGCCA CGATCATGGAGGAGTTGGCAGATGC AXIN2 223 ACCAGCGCCAACGACAGTGAGATA 224 GGCTATGTCTTTGCACCAGCCACCAGCGCCAACGACAGTGAG ATATCCAGTGATGCGCTGACGGAT AZGP1 227 TCTGAGATCCCACATTGCCTCCAA 228 GAGGCCAGCTAGGAAGCAAGGGTTGGAGGCAATGTGGGATCT CAGACCCAGTAGCTGCCCTTCCTG BAD 231 TGGGCCCAGAGCATGTTCCAGATC 232 GGGTCAGGGGCCTCGAGATCGGGCTTGGGCCCAGAGCATGTT CCAGATCCCAGAGTTTGAGCCGAGTGAGCAG BAG5 235 ACACCGGATTTAGCTCTTGTCGGC 236 ACTCCTGCAATGAACCCTGTTGACACCGGATTTAGCTCTTGTC GGCCTTCGTGGGGAGCTGTTTGT BAK1 239 ACACCCCAGACGTCCTGGCCT 240 CCATTCCCACCATTCTACCTGAGGCCAGGACGTCTGGGGTGT GGGGATTGGTGGGTCTATGTTCCC BAX 243 TGCCACTCGGAAAAAGACCTCTCGG 244 CCGCCGTGGACACAGACTCCCCCCGAGAGGTCTTTTTCCGAG TGGCAGCTGACATGTTTTCTGACGGCAA BBC3 247 CATCATGGGACTCCTGCCCTTACC 248 CCTGGAGGGTCCTGTACAATCTCATCATGGGACTCCTGCCCTT ACCCAGGGGCCACAGAGCCCCCGAGATGGAGCCCAATTAG BCL2 251 TTCCACGCCGAAGGACAGCGAT 252 CAGATGGACCTAGTACCCACTGAGATTTCCACGCCGAAGGAC AGCGATGGGAAAAATGCCCTTAAATCATAGG BDKRB1 255 ACCTGGCAGCCTCTGATCTGGTGT 256 GTGGCAGAAATCTACCTGGCCAACCTGGCAGCCTCTGATCTG GTGTTTGTCTTGGGCTTGCCCTTC BGN 259 CAAGGGTCTCCAGCACCTCTACGC 260 GAGCTCCGCAAGGATGACTTCAAGGGTCTCCAGCACCTCTAC GCCCTCGTCCTGGTGAACAACAAG BIK 263 CCGGTTAACTGTGGCCTGTGCCC 264 ATTCCTATGGCTCTGCAATTGTCACCGGTTAACTGTGGCCTGT GCCCAGGAAGAGCCATTCACTCCTGCC BIN1 267 CTTCGCCTCCAGATGGCTCCC 268 CCTGCAAAAGGGAACAAGAGCCCTTCGCCTCCAGATGGCTCC CCTGCCGCCACCCCCGAGATCAGAGTCAACCACG BIRC5 271 TCTGCCAGACGCTTCCTATCACTCTATTC 272 TTCAGGTGGATGAGGAGACAGAATAGAGTGATAGGAAGCGTC TGGCAGATACTCCTTTTGCCACTGCTGTGTG BMP6 275 TGAACCCCGAGTATGTCCCCAAAC 276 GTGCAGACCTTGGTTCACCTTATGAACCCCGAGTATGTCCCCA AACCGTGCTGTGCGCCAACTAAG BMPR1B 279 ATTCACATTACCATAGCGGCCCCA 280 ACCACTTTGGCCATCCCTGCATTTGGGGCCGCTATGGTAATGT GAATGCACTGGGTACAAACACCGC BRCA1 283 CTATGGGCCCTTCACCAACATGC 284 TCAGGGGGCTAGAAATCTGTTGCTATGGGCCCTTCACCAACAT GCCCACAGATCAACTGGAATGG BRCA2 287 CATTCTTCACTGCTTCATAAAGCTCTGCA 288 AGTTCGTGCTTTGCAAGATGGTGCAGAGCTTTATGAAGCAGTG AAGAATGCAGCAGACCCAGCTTACCTT BTG1 291 CGCTCGTCTCTTCCTCTCTCCTGC 292 GAGGTCCGAGCGATGTGACCAGGCCGCCATCGCTCGTCTCTT CCTCTCTCCTGCCGCCTCCTGTCTCGAAAATAACT BTG3 295 CATGGGTACCTCCTCCTGGAATGC 296 CCATATCGCCCAATTCCAGTGACATGGGTACCTCCTCCTGGAA TGCATTGTGACCGGAATCACTGG BTRC 299 CAGTCGGCCCAGGACGGTCTACT 300 GTTGGGACACAGTTGGTCTGCAGTCGGCCCAGGACGGTCTAC TCAGCACAACTGACTGCTTCA BUB1 303 TGCTGGGAGCCTACACTTGGCCC 304 CCGAGGTTAATCCAGCACGTATGGGGCCAAGTGTAGGCTCCC AGCAGGAACTGAGAGCGCCATGTCTT C7 307 ATGCTCTGCCCTCTGCATCTCAGA 308 ATGTCTGAGTGTGAGGCGGGCGCTCTGAGATGCAGAGGGCAG AGCATCTCTGTCACCAGCATAAGGCCT CACNA1D 311 CAGTACACTGGCGTCCATTCCCTG 312 AGGACCCAGCTCCATGTGCGTTCTCAGGGAATGGACGCCAGT GTACTGCCAATGGCACGGAATGTAGG CADM1 315 TCTTCACCTGCTCGGGAATCTGTG 316 CCACCACCATCCTTACCATCATCACAGATTCCCGAGCAGGTGA AGAAGGCTCGATCAGGGCAGTGGATC CADPS 319 CTCCTGGATGGCCAAATTTGATGC 320 CAGCAAGGAGACTGTGCTGAGCTCCTGGATGGCCAAATTTGAT GCCATCTACCGTGGAGAAGAGGACC CASP1 323 TCACAGGCATGACAATGCTGCTACA 324 AACTGGAGCTGAGGTTGACATCACAGGCATGACAATGCTGCTA CAAAATCTGGGGTACAGCGTAGATG CASP3 327 TCAGCCTGTTCCATGAAGGCAGAGC 328 TGAGCCTGAGCAGAGACATGACTCAGCCTGTTCCATGAAGGC AGAGCCATGGACCACGCAGGAAGG CASP7 331 CTTTCGCTAAAGGGGCCCCAGAC 332 GCAGCGCCGAGACTTTTAGTTTCGCTTTCGCTAAAGGGGCCCC AGACCCTTGCTGCGGAGCGACGGAGAGAGACT CAV1 335 ATTTCAGCTGATCAGTGGGCCTCC 336 GTGGCTCAACATTGTGTTCCCATTTCAGCTGATCAGTGGGCCT CCAAGGAGGGGCTGTAAAATGGAGGCCATTG CAV2 339 CCCGTACTGTCATGCCTCAGAGCT 340 CTTCCCTGGGACGACTTGCCAGCTCTGAGGCATGACAGTACG GGCCCCCAGAAGGGTGACCAGGAG CCL2 343 TGCCCCAGTCACCTGCTGTTA 344 CGCTCAGCCAGATGCAATCAATGCCCCAGTCACCTGCTGTTAT AACTTCACCAATAGGAAGATCTCAGTGC CCL5 347 ACAGAGCCCTGGCAAAGCCAAG 348 AGGTTCTGAGCTCTGGCTTTGCCTTGGCTTTGCCAGGGCTCTG TGACCAGGAAGGAAGTCAGCAT CCNB1 351 TGTCTCCATTATTGATCGGTTCATGCA 352 TTCAGGTTGTTGCAGGAGACCATGTACATGACTGTCTCCATTAT TGATCGGTTCATGCAGAATAATTGTGTGCCCAAGAAGATG CCND1 355 AAGGAGACCATCCCCCTGACGGC 356 GCATGTTCGTGGCCTCTAAGATGAAGGAGACCATCCCCCTGA CGGCCGAGAAGCTGTGCATCTACACCG CCNE2 359 TACCAAGCAACCTACATGTCAAGAAAGC 360 ATGCTGTGGCTCCTTCCTAACTGGGGCTTTCTTGACATGTAGG CC TTGCTTGGTAATAACCTTTTTGTATATCACAATTTGGGT CCNH 363 CATCAGCGTCCTGGCGTAAAACAC 364 GAGATCTTCGGTGGGGGTACGGGTGTTTTACGCCAGGACGCT GATGCGTTTGGGTTCTCGTCTGCAG CCR1 367 ACTCACCACACCTGCAGCCTTCAC 368 TCCAAGACCCAATGGGAATTCACTCACCACACCTGCAGCCTTC ACTTTCCTCACGAAAGCCTACGA CD164 371 CCTCCAATGAAACTGGCTGCATCA 372 CAACCTGTGCGAAAGTCTACCTTTGATGCAGCCAGTTTCATTG GAGGAATTGTCCTGGTCTTGGGTGT CD1A 375 CGCACCATTCGGTCATTTGAGG 376 GGAGTGGAAGGAACTGGAAACATTATTCCGTATACGCACCATT CGGTCATTTGAGGGAATTCGTAGATACGCCCATGA CD276 379 CCACTGTGCAGCCTTATTTCTCCAATG 380 CCAAAGGATGCGATACACAGACCACTGTGCAGCCTTATTTCTC CAATGGACATGATTCCCAAGTCATCC CD44 383 ACTGGAACCCAGAAGCACACCCTC 384 GGCACCACTGCTTATGAAGGAAACTGGAACCCAGAAGCACAC CCTCCCCTCATTCACCATGAGCATC CD68 387 CTCCAAGCCCAGATTCAGATTCGAGTCA 388 TGGTTCCCAGCCCTGTGTCCACCTCCAAGCCCAGATTCAGATT CGAGTCATGTACACAACCCAGGGTGGAGGAG CD82 391 TCAGCTTCTACAACTGGACAGACAACGC 392 GTGCAGGCTCAGGTGAAGTGCTGCGGCTGGGTCAGCTTCTAC TG AACTGGACAGACAACGCTGAGCTCATGAATCGCCCTGAGGTC CDC20 395 ACTGGCCGTGGCACTGGACAACA 396 TGGATTGGAGTTCTGGGAATGTACTGGCCGTGGCACTGGACA ACAGTGTGTACCTGTGGAGTGCAAGC CDC25B 399 CTGCTACCTCCCTTGCCTTTCGAG 400 GCTGCAGGACCAGTGAGGGGCCTGCGCCAGTCCTGCTACCTC CCTTGCCTTTCGAGGCCTGAAGCCAGCTGCCCTA CDC6 403 TTGTTCTCCACCAAAGCAAGGCAA 404 GCAACACTCCCCATTTACCTCCTTGTTCTCCACCAAAGCAAGG CAAGAAAGAGAATGGTCCCCCTCA CDH1 407 TGCCAATCCCGATGAAATTGGAAATTT 408 TGAGTGTCCCCCGGTATCTTCCCCGCCCTGCCAATCCCGATGA AATTGGAAATTTTATTGATGAAAATCTGAAAGCGGCTG CDH10 411 ATGCCGATGACCCTTCATATGGGA 412 TGTGGTGCAAGTCACAGCTACAGATGCCGATGACCCTTCATAT GGGAACAGCGCCAGAGTCATTTACA CDH11 415 CCTTCTGCCCATAGTGATCAGCGA 416 GTCGGCAGAAGCAGGACTTGTACCTTCTGCCCATAGTGATCAG CGATGGCGGCATCCCGCCCATGAGTAG CDH19 419 ACTCGGAAAACCACAAGCGCTGAG 420 AGTACCATAATGCGGGAACGCAAGACTCGGAAAACCACAAGC GCTGAGATCAGGAGCCTATACAGGCAGTCT CDH5 423 TATTCTCCCGGTCCAGCCTCTCAA 424 ACAGGAGACGTGTTCGCCATTGAGAGGCTGGACCGGGAGAAT ATCTCAGAGTACCACCTCACTGCTG CDH7 427 ACCTCAACGTCATCCGAGACACCA 428 GTTTGACATGGCTGCACTGAGAAACCTCAACGTCATCCGAGAC ACCAAGACCCGGAGGGATGTGACT CDK14 431 CTTCCTGCAGCCTGATCACCTTCA 432 GCAAGGTAAATGGGAAGTTGGTAGCTCTGAAGGTGATCAGGC TGCAGGAAGAAGAAGGGACACCTTTCACAGCTATC CDK2 435 CCTTGGCCGAAATCCGCTTGT 436 AATGCTGCACTACGACCCTAACAAGCGGATTTCGGCCAAGGC AGCCCTGGCTCACCCTTTCTTCCAGGATGTGACCAA CDK3 439 CTCTGGCTCCAGATTGGGCACAAT 440 CCAGGAAGGGACTGGAAGAGATTGTGCCCAATCTGGAGCCAG AGGGCAGGGACCTGCTCATGCAAC CDK7 443 CCTCCCCAAGGAAGTCCAGCTTCT 444 GTCTCGGGCAAAGCGTTATGAGAAGCTGGACTTCCTTGGGGA GGGACAGTTTGCCACCGTTTACAAGGCCAGAG CDKN1A 447 CGGCGGCAGACCAGCATGAC 448 TGGAGACTCTCAGGGTCGAAAACGGCGGCAGACCAGCATGAC AGATTTCTACCACTCCAAACGCC CDKN1C 451 CGGGCCTCTGATCTCCGATTTCTT 452 CGGCGATCAAGAAGCTGTCCGGGCCTCTGATCTCCGATTTCTT CGCCAAGCGCAAGAGATCAGCGCCTG CDKN2B 455 CACAGGATGCTGGCCTTTGCTCTT 456 GACGCTGCAGAGCACCTTTGCACAGGATGCTGGCCTTTGCTCT TACTACACTGAGGAGAGATTCCCGC CDKN2C 459 CCTGTAACTTGAGGGCCACCGAAC 460 GAGCACTGGGCAATCGTTACGACCTGTAACTTGAGGGCCACC GAACTGCTACTCCCGTTCGCCTTTG CDKN3 463 ATCACCCATCATCATCCAATCGCA 464 TGGATCTCTACCAGCAATGTGGAATTATCACCCATCATCATCC AATCGCAGATGGAGGGACTCCTGACAT CDS2 467 CCCGGACATCACATAGGACAGCAG 468 GGGCTTCTTTGCTACTGTGGTGTTTGGCCTTCTGCTGTCCTAT GTGATGTCCGGGTACAGATGCTTTGTCTGCCCTGT CENPF 471 ACACTGGACCAGGAGTGCATCCAG 472 CTCCCGTCAACAGCGTTCTTTCCAAACACTGGACCAGGAGTGC ATCCAGATGAAGGCCAGACTCACCC CHAF1A 475 TGCACGTACCAGCACATCCTGAAG 476 GAACTCAGTGTATGAGAAGCGGCCTGACTTCAGGATGTGCTG GTACGTGCACCCGCAGGTGCTACAGAGC CHN1 479 CCACCATTGGCCGCTTAGTGGTAT 480 TTACGACGCTCGTGAAAGCACATACCACTAAGCGGCCAATGGT GGTAGACATGTGCATCAGGGAGA CHRAC1 483 ATCCGGGTCATCATGAAGAGCTCC 484 TCTCGCTGCCTCTATCCCGCATCCGGGTCATCATGAAGAGCTC CCCCGAGGTGTCCAGCATCAACCAGG CKS2 487 CTGCGCCCGCTCTTCGCG 488 GGCTGGACGTGGTTTTGTCTGCTGCGCCCGCTCTTCGCGCTCT CGTTTCATTTTCTGCAGCG CLDN3 491 CAAGGCCAAGATCACCATCGTGG 492 ACCAACTGCGTGCAGGACGACACGGCCAAGGCCAAGATCACC ATCGTGGCAGGCGTGCTGTTCCTTCTCGCC CLTC 495 TCTCACATGCTGTACCCAAAGCCA 496 ACCGTATGGACAGCCACAGCCTGGCTTTGGGTACAGCATGTG AGATGAAGCGCTGATCCTGTAGTCA COL11A1 499 CTGCTCGACCTTTGGGTCCTTCAG 500 GCCCAAGAGGGGAAGATGGCCCTGAAGGACCCAAAGGTCGA GCAGGCCCAACTGGAGACCCAGGTCC COL1A1 503 TCCTGCGCCTGATGTCCACCG 504 GTGGCCATCCAGCTGACCTTCCTGCGCCTGATGTCCACCGAG GCCTCCCAGAACATCACCTACCACTG COL1A2 507 TCTCCTAGCCAGACGTGTTTCTTGTCCT 508 CAGCCAAGAACTGGTATAGGAGCTCCAAGGACAAGAAACACG TG TCTGGCTAGGAGAAACTATCAATGCTGGCAGCCAGTTT COL3A1 511 CTCCTGGTCCCCAAGGTGTCAAAG 512 GGAGGTTCTGGACCTGCTGGTCCTCCTGGTCCCCAAGGTGTC AAAGGTGAACGTGGCAGTCCTGGT COL4A1 515 CTCCTTTGACACCAGGGATGCCAT 516 ACAAAGGCCTCCCAGGATTGGATGGCATCCCTGGTGTCAAAG GAGAAGCAGGTCTTCCTGGGACTC COL5A1 519 CCAGGGAAACCACGTAATCCTGGA 520 CTCCCTGGGAAAGATGGCCCTCCAGGATTACGTGGTTTCCCTG GGGACCGAGGGCTTCCTGGTCCAG COL5A2 523 CCAGGAAATCCTGTAGCACCAGGC 524 GGTCGAGGAACCCAAGGTCCGCCTGGTGCTACAGGATTTCCT GGTTCTGCGGGCAGAGTTGGACCTCCAGGC COL6A1 527 CTTCTCTTCCCTGATCACCCTGCG 528 GGAGACCCTGGTGAAGCTGGCCCGCAGGGTGATCAGGGAAG AGAAGGCCCCGTTGGTGTCCCTGGAGA COL6A3 531 CCTCTTTGACGGCTCAGCCAATCT 532 GAGAGCAAGCGAGACATTCTGTTCCTCTTTGACGGCTCAGCCA ATCTTGTGGGCCAGTTCCCTGTT COL8A1 535 CCTAAGGGAGAGCCAGGAATCCCA 536 TGGTGTTCCAGGGCTTCTCGGACCTAAGGGAGAGCCAGGAAT CCCAGGGGATCAGGGTTTACAGGG COL9A2 539 ACACAGGAAATCCGCACTGCCTTC 540 GGGAACCATCCAGGGTCTGGAAGGCAGTGCGGATTTCCTGTG TCCAACCAACTGTCCACCCGGAAT CRISP3 543 TGCCAGTTGCCCAGATAACTGTGA 544 TCCCTTATGAACAAGGAGCACCTTGTGCCAGTTGCCCAGATAA CTGTGACGATGGACTATGCACCAATGGTT CSF1 547 TCAGATGGAGACCTCGTGCCAAATTACA 548 TGCAGCGGCTGATTGACAGTCAGATGGAGACCTCGTGCCAAA TTACATTTGAGTTTGTAGACCAGGAACAGTTG CSK 551 TCCCGATGGTCTGCAGCAGCT 552 CCTGAACATGAAGGAGCTGAAGCTGCTGCAGACCATCGGGAA GGGGGAGTTCGGAGACGTGATG CSRP1 555 CCACCCTTCTCCAGGGACCCTTAG 556 ACCCAAGACCCTGCCTCTTCCACTCCACCCTTCTCCAGGGACC CTTAGATCACATCACTCCACCCCTGC CTGF 559 AACATCATGTTCTTCTTCATGACCTCGC 560 GAGTTCAAGTGCCCTGACGGCGAGGTCATGAAGAAGAACATG ATGTTCATCAAGACCTGTGCCTGCCATTACAACT CTHRC1 563 CAACGCTGACAGCATGCATTTCTG 564 TGGCTCACTTCGGCTAAAATGCAGAAATGCATGCTGTCAGCGT TGGTATTTCACATTCAATGGAGCTGA CTNNA1 567 ATGCCTACAGCACCCTGATGTCGCA 568 CGTTCCGATCCTCTATACTGCATCCCAGGCATGCCTACAGCAC CCTGATGTCGCAGCCTATAAGGCCAACAGGGACCT CTNNB1 571 AGGCTCAGTGATGTCTTCCCTGTCACCAG 572 GGCTCTTGTGCGTACTGTCCTTCGGGCTGGTGACAGGGAAGA CATCACTGAGCCTGCCATCTGTGCTCTTCGTCATCTGA CTNND1 575 TTGATGCCCTCATTTTCATTGTTCAGGC 576 CGGAAACTTCGGGAATGTGATGGTTTAGTTGATGCCCTCATTT TCATTGTTCAGGCTGAGATTGGGCAGAAGGATTCAG CTNND2 579 CTATGAAACGAGCCACTACCCGGC 580 GCCCGTCCCTACAGTGAACTGAACTATGAAACGAGCCACTACC CGGCCTCCCCCGACTCCTGGGTGTGAG CTSB 583 CCCCGTGGAGGGAGCTTTCTC 584 GGCCGAGATCTACAAAAACGGCCCCGTGGAGGGAGCTTTCTC TGTGTATTCGGACTTCCTGC CTSD 587 ACCCTGCCCGCGATCACACTGA 588 GTACATGATCCCCTGTGAGAAGGTGTCCACCCTGCCCGCGAT CACACTGAAGCTGGGAGGCAAAGGCTACAAGCTGTCCC CTSK 591 CCCCAGGTGGTTCATAGCCAGTTC 592 AGGCTTCTCTTGGTGTCCATACATATGAACTGGCTATGAACCA CCTGGGGGACATGACCAGTGAAGAGGTGG CTSL2 595 CTTGAGGACGCGAACAGTCCACCA 596 TGTCTCACTGAGCGAGCAGAATCTGGTGGACTGTTCGCGTCCT CAAGGCAATCAGGGCTGCAATGGT CTSS 599 TGATAACAAGGGCATCGACTCAGACGCT 600 TGACAACGGCTTTCCAGTACATCATTGATAACAAGGGCATCGA CTCAGACGCTTCCTATCCCTACAAAGCCATGGA CUL1 603 CAGCCACAAAGCCAGCGTCATTGT 604 ATGCCCTGGTAATGTCTGCATTCAACAATGACGCTGGCTTTGT GGCTGCTCTTGATAAGGCTTGTGGTCGC CXCL12 607 TTCTTCGAAAGCCATGTTGCCAGA 608 GAGCTACAGATGCCCATGCCGATTCTTCGAAAGCCATGTTGCC AGAGCCAACGTCAAGCATCTCAAA CXCR4 611 CTGAAACTGGAACACAACCACCCACAAG 612 TGACCGCTTCTACCCCAATGACTTGTGGGTGGTTGTGTTCCAG TTTCAGCACATCATGGTTGGCCTTATCCT CXCR7 615 CTCAGAGCCAGGGAACTTCTCGGA 616 CGCCTCAGAACGATGGATCTGCATCTCTTCGACTACTCAGAGC CAGGGAACTTCTCGGACATCAGCTGGCCATGCAAC CYP3A5 619 TCCCGCCTCAAGTTTCTCACCAAT 620 TCATTGCCCAGTATGGAGATGTATTGGTGAGAAACTTGAGGCG GGAAGCAGAGAAAGGCAAGCCTGTC CYR61 623 CAGCACCCTTGGCAGTTTCGAAAT 624 TGCTCATTCTTGAGGAGCATTAAGGTATTTCGAAACTGCCAAG GGTGCTGGTGCGGATGGACACTAATGCAGCCAC DAG1 627 CAAGTCAGAGTTTCCCTGGTGCCC 628 GTGACTGGGCTCATGCCTCCAAGTCAGAGTTTCCCTGGTGCC CCAGAGACAGGAGCACAAGTGGGAT DAP 631 CTCACCAGCTGGCAGACGTGAACT 632 CCAGCCTTTCTGGTGCTGTTCTCCAGTTCACGTCTGCCAGCTG GTGAGGGCAGAGGCAGACCTGGTC DAPK1 635 TCATATCCAAACTCGCCTCCAGCCG 636 CGCTGACATCATGAATGTTCCTCGACCGGCTGGAGGCGAGTTT GGATATGACAAAGACACATCGTTGCTGAAAGAGA DARC 639 TCAGCGCCTGTGCTTCCAAGATAA 640 GCCCTCATTAGTCCTTGGCTCTTATCTTGGAAGCACAGGCGCT GACAGCCGTCCCAGCCCTTCTGTCTG DDIT4 643 CTAGCCTTTGGGACCGCTTCTCGT 644 CCTGGCGTCTGTCCTCACCATGCCTAGCCTTTGGGACCGCTTC TCGTCGTCGTCCACCTCCTCTTCG DDR2 647 AGTGCTCCCTATCCGCTGGATGTC 648 CTATTACCGGATCCAGGGCCGGGCAGTGCTCCCTATCCGCTG GATGTCTTGGGAGAGTATCTTGCTGGG DES 651 TGAACCAGGAGTTTCTGACCACGC 652 ACTTCTCACTGGCCGACGCGGTGAACCAGGAGTTTCTGACCA CGCGCACCAACGAGAAGGTGGAGC DHRS9 655 ATCAATAATGCTGGTGTTCCCGGC 656 GGAGAAAGGTCTCTGGGGTCTGATCAATAATGCTGGTGTTCCC GGCGTGCTGGCTCCCACTGACTG DHX9 659 CCAAGGAACCACACCCACTTGGTT 660 GTTCGAACCATCTCAGCGACAAAACCAAGTGGGTGTGGTTCCT TGGTCACCTCCACAATCCAACTGGA DIAPH1 663 TTCTTCTGTCTCCCGCCGCTTC 664 CAAGCAGTCAAGGAGAACCAGAAGCGGCGGGAGACAGAAGA AAAGATGAGGCGAGCAAAACT DICER1 667 AGAAAAGCTGTTTGTCTCCCCAGCA 668 TCCAATTCCAGCATCACTGTGGAGAAAAGCTGTTTGTCTCCCC AGCATACTTTATCGCCTTCACTGCC DIO2 671 ACTCTTCCACCAGTTTGCGGAAGG 672 CTCCTTTCACGAGCCAGCTGCCAGCCTTCCGCAAACTGGTGG AAGAGTTCTCCTCAGTGGCTGACTTCCT DLC1 675 AAAGTCCATTTGCCACTGATGGCA 676 GATTCAGACGAGGATGAGCCTTGTGCCATCAGTGGCAAATGG ACTTTCCAAAGGGACAGCAAGAGGTG DLGAP1 679 CGCAGACCACCCATACTACACCCA 680 CTGCTGAGCCCAGTGGAGCACCACCCCGCAGACCACCCATAC TACACCCAGCGGAACTCCTTCCAGGCT DLL4 683 CTACCTGGACATCCCTGCTCAGCC 684 CACGGAGGTATAAGGCAGGAGCCTACCTGGACATCCCTGCTC AGCCCCGCGGCTGGACCTTCCTTCT DNM3 687 CATATCGCTGACCGAATGGGAACC 688 CTTTCCCACCCGGCTTACAGACATATCGCTGACCGAATGGGAA CCCCACACCTGCAGAAGGTCCTT DPP4 691 CGGCTATTCCACACTTGAACACGC 692 GTCCTGGGATCGGGAAGTGGCGTGTTCAAGTGTGGAATAGCC GTGGCGCCTGTATCCCGGTGGGAGTAC DPT 695 TTCCTAGGAAGGCTGGCAGACACC 696 CACCTAGAAGCCTGCCCACGATTCCTAGGAAGGCTGGCAGAC ACCCTGGAACCCTGGGGAGCTACTG DUSP1 699 CGAGGCCATTGACTTCATAGACTCCA 700 AGACATCAGCTCCTGGTTCAACGAGGCCATTGACTTCATAGAC TCCATCAAGAATGCTGGAGGAAGGGTGTTTGTC DUSP6 703 TCTACCCTATGCGCCTGGAAGTCC 704 CATGCAGGGACTGGGATTCGAGGACTTCCAGGCGCATAGGGT AGAACCAAATGATAGGGTAGGAGCA DVL1 707 CTTGGAGCAGCCTGCACCTTCTCT 708 TCTGTCCCACCTGCTGCTGCCCCTTGGAGCAGCCTGCACCTTC TCTCCTCCCATCCGGCAACAGTCTGA DYNLL1 711 ACCCACGTCAGTGAGTGCTCACAA 712 GCCGCCTACCTCACAGACTTGTGAGCACTCACTGACGTGGGT AGCGCCCAGGGCCTGCGGGGCGCAGGAGAGCTGGAGTCAGG C EBNA1BP2 715 CCCGCTCTCGGATTCGGAGTCG 716 TGCGGCGAGATGGACACTCCCCCGCTCTCGGATTCGGAGTCG GAATCCGATGAATCCCTTGTCAC ECE1 719 TCCACTCTCGATACCCTGCACCAG 720 ACCTTGGGATCTGCCTCCAAGCTGGTGCAGGGTATCGAGAGT GGATTCCAGATGGAGGTCCTGGTCC EDN1 723 CACTCCCGAGCACGTTGTTCCGT 724 TGCCACCTGGACATCATTTGGGTCAACACTCCCGAGCACGTTG TTCCGTATGGACTTGGAAGCCCTAGGTCCA EDNRA 727 CCTTTGCCTCAGGGCATCCTTTT 728 TTTCCTCAAATTTGCCTCAAGATGGAAACCCTTTGCCTCAGGG CATCCTTTTGGCTGGCACTGGTTGGATGTGTAA EFNB2 731 CGGACAGCGTCTTCTGCCCTCACT 732 TGACATTATCATCCCGCTAAGGACTGCGGACAGCGTCTTCTGC CCTCACTACGAGAAGGTCAGCGGGGACTAC EGF 735 AGAGTTTAACAGCCCTGCTCTGGCTGAC 736 CTTTGCCTTGCTCTGTCACAGTGAAGTCAGCCAGAGCAGGGCT TT GTTAAACTCTGTGAAATTTGTCATAAGGGTGTCAGGTATTT EGR1 739 CGGATCCTTTCCTCACTCGCCCA 740 GTCCCCGCTGCAGATCTCTGACCCGTTCGGATCCTTTCCTCAC TCGCCCACCATGGACAACTACCCTAAGCTGGAG EGR3 743 ACCCAGTCTCACCTTCTCCCCACC 744 CCATGTGGATGAATGAGGTGTCTCCTTTCCATACCCAGTCTCA CCTTCTCCCCACCCTACCTCACCTCTTCTCAGGCA EIF2C2 747 CGGGTCACATTGCAGACACGGTAC 748 GCACTGTGGGCAGATGAAGAGGAAGTACCGCGTCTGCAATGT GACCCGGCGGCCCGCCAGTCACCAAACAT EIF2S3 751 TCTCGTGCTTCAGCCTCCCATGTA 752 CTGCCTCCCTGATTCAAGTGATTCTCGTGCTTCAGCCTCCCAT GTAGCTGATATTACAGGCACTTGCCACC EIF3H 755 CAGAACATCAAGGAGTTCACTGCCCA 756 CTCATTGCAGGCCAGATAAACACTTACTGCCAGAACATCAAGG AGTTCACTGCCCAAAACTTAGGCAAGCTCTTCATGGC EIF4E 759 ACCACCCCTACTCCTAATCCCCCGACT 760 GATCTAAGATGGCGACTGTCGAACCGGAAACCACCCCTACTC CTAATCCCCCGACTACAGAAGAGGAGAAAACGGAATCTAA EIF5 763 CCACTTGCACCCGAATCTTGATCA 764 GAATTGGTCTCCAGCTGCCTTTGATCAAGATTCGGGTGCAAGT GGAGCAGGAGCCATATACCTGGA ELK4 767 ATAAACCACCTCAGCCTGGTGCCA 768 GATGTGGAGAATGGAGGGAAAGATAAACCACCTCAGCCTGGT GCCAAGACCTCTAGCCGCAATGACT ENPP2 771 TAACTTCCTCTGGCATGGTTGGCC 772 CTCCTGCGCACTAATACCTTCAGGCCAACCATGCCAGAGGAA GTTACCAGACCCAATTATCCAGGGA ENY2 775 CTGATCCTTCCAGCCACATTCAATTAAT 776 CCTCAAAGAGTTGCTGAGAGCTAAATTAATTGAATGTGGCTGG TT AAGGATCAGTTGAAGGCACACTGTAAAGAGG EPHA2 779 TGCGCCCGATGAGATCACCG 780 CGCCTGTTCACCAAGATTGACACCATTGCGCCCGATGAGATCA CCGTCAGCAGCGACTTCGAGGCACGCCAC EPHA3 783 TATTCCAAATCCGAGCCCGAACAG 784 CAGTAGCCTCAAGCCTGACACTATATACGTATTCCAAATCCGA GCCCGAACAGCCGCTGGATATGGGACGAA EPHB2 787 CACCTGATGCATGATGGACACTGC 788 CAACCAGGCAGCTCCATCGGCAGTGTCCATCATGCATCAGGT GAGCCGCACCGTGGACAGCATTAC EPHB4 791 CGTCCCATTTGAGCCTGTCAATGT 792 TGAACGGGGTATCCTCCTTAGCCACGGGGCCCGTCCCATTTG AGCCTGTCAATGTCACCACTGACCGAGAGGTACCT ERBB2 795 CCAGACCATAGCACACTCGGGCAC 796 CGGTGTGAGAAGTGCAGCAAGCCCTGTGCCCGAGTGTGCTAT GGTCTGGGCATGGAGCACTTGCGAGAGG ERBB3 799 CCTCAAAGGTACTCCCTCCTCCCGG 800 CGGTTATGTCATGCCAGATACACACCTCAAAGGTACTCCCTCC TCCCGGGAAGGCACCCTTTCTTCAGTGGGTCTCAGTTC ERBB4 803 TGTCCCACGAATAATGCGTAAATTCTCC 804 TGGCTCTTAATCAGTTTCGTTACCTGCCTCTGGAGAATTTACGC AG ATTATTCGTGGGACAAAACTTTATGAGGATCGATATGCCTTG ERCC1 807 CAGCAGGCCCTCAAGGAGCTG 808 GTCCAGGTGGATGTGAAAGATCCCCAGCAGGCCCTCAAGGAG CTGGCTAAGATGTGTATCCTGGCCG EREG 811 TAAGCCATGGCTGACCTCTGGAGC 812 TGCTAGGGTAAACGAAGGCATAATAAGCCATGGCTGACCTCTG GAGCACCAGGTGCCAGGACTTGTCTCCA ERG 815 AGCCATATGCCTTCTCATCTGGGC 816 CCAACACTAGGCTCCCCACCAGCCATATGCCTTCTCATCTGGG CACTTACTACTAAAGACCTGGCGGAGG ESR1 819 CTGGAGATGCTGGACGCCC 820 CGTGGTGCCCCTCTATGACCTGCTGCTGGAGATGCTGGACGC CCACCGCCTACATGCGCCCACTAGCC ESR2 823 ATCTGTATGCGGAACCTCAAAAGAGTCC 824 TGGTCCATCGCCAGTTATCACATCTGTATGCGGAACCTCAAAA CT GAGTCCCTGGTGTGAAGCAAGATCGCTAGAACA ETV1 827 ATCGGGAAGGACCCACATACCAAC 828 TCAAACAAGAGCCAGGAATGTATCGGGAAGGACCCACATACC AACGGCGAGGATCACTTCAGCTCTGGCAGTT ETV4 831 CAGACAAATCGCCATCAAGTCCCC 832 TCCAGTGCCTATGACCCCCCCAGACAAATCGCCATCAAGTCCC CTGCCCCTGGTGCCCTTGGACAGT EZH2 835 TCCTGACTTCTGTGAGCTCATTGCG 836 TGGAAACAGCGAAGGATACAGCCTGTGCACATCCTGACTTCTG TGAGCTCATTGCGCGGGACTAGGGAGTGTTCGGTG F2R 839 CCCGGGCTCAACATCACTACCTGT 840 AAGGAGCAAACCATCCAGGTGCCCGGGCTCAACATCACTACC TGTCATGATGTGCTCAATGAAACCCTGC FAH 843 TGCCCTTCGTGCACACCAATG 844 GACAGCGTAGTGGTGCATGTGCTGAAGCTGCAGGGTGCCGTG CCCTTCGTGCACACCAATGTTCCACAGTCCATGTTCAGCT FABP5 847 CCTGATGCTGAACCAATGCACCAT 848 GCTGATGGCAGAAAAACTCAGACTGTCTGCAACTTTACAGATG GTGCATTGGTTCAGCATCAGGAGTGGGATGGGAAGGAAAG FADD 851 AACGCGCTCTTGTCGATTTCCTGT 852 GrITTCGCGAGATAACGGTCGAAAACGCGCTCTTGTCGATTTC CTGTAGTGAATCAGGCACCGGAG FAM107A 855 AATTGCCACACTGACCAGCGAAGA 856 AAGTCAGGGAAAACCTGCGGAGAATTGCCACACTGACCAGCG AAGAGAGAGAGCTGTAGGGCCAGC FAM13C 859 TCCTGACTTTCTCCGTGGCTCCTC 860 ATCTTCAAAGCGGAGAGCGGGAGGAGCCACGGAGAAAGTCAG GAGACAGAGCATGTGGTATCCAGC FAM171B 863 TGAAGATTTTGAAGCTAATACATCCCCC 864 CCAGGAAGGAAAAGCACTGTTGAAGATTTTGAAGCTAATACAT AC CCCCCACTAAAAGAAGGGGCAGACCAC FAM49B 867 TGGCCAGCTCCTCTGTATGACTGC 868 AGATGCAGAAGGCATCTTGGAGGACTTGCAGTCATACAGAGG AGCTGGCCACGAAATACGAGAGGCAATCCAGC FAM73A 871 AAGACCTCATGCAGTTACTCATTCGCC 872 TGAGAAGGTGCGCTATTCAAGTACAGAGACTTTAGCTGAAGAC CTCATGCAGTTACTCATTCGCCGCACTGAGCTTTTAATGGCC FAP 875 AGCCACTGCAAACATACTCGTTCATCA 876 GTTGGCTCACGTGGGTTACTGATGAACGAGTATGTTTGCAGTG GCTAAAAAGAGTCCAGAATGTTTCGGTCCTGTC FAS 879 TCTGGACCCTCCTACCTCTGGTTCTTAC 880 GGATTGCTCAACAACCATGCTGGGCATCTGGACCCTCCTACCT GT CTGGTTCTTACGTCTGTTGCTAGATTATCGTCCAAAAGTGTTAA TGCC FASLG 883 ACAACATTCTCGGTGCCTGTAACAAAGAA 884 GCACTTTGGGATTCTTTCCATTATGATTCTTTGTTACAGGCACC GAGAATGTTGTATTCAGTGAGGGTCTTCTTACATGC FASN 887 TCGCCCACCTACGTACTGGCCTAC 888 GCCTCTTCCTGTTCGACGGCTCGCCCACCTACGTACTGGCCTA CACCCAGAGCTACCGGGCAAAGC FCGR3A 891 CCCATGATCTTCAAGCAGGGAAGC 892 GTCTCCAGTGGAAGGGAAAAGCCCATGATCTTCAAGCAGGGA AGCCCCAGTGAGTAGCTGCATTCCT FGF10 895 ACACCATGTCCTGACCAAGGGCTT 896 TCTTCCGTCCCTGTCACCTGCCAAGCCCTTGGTCAGGACATGG TGTCACCAGAGGCCACCAACTCT FGF17 899 TTCTCGGATCTCCCTCAGTCTGCC 900 GGTGGCTGTCCTCAAAATCTGCTTCTCGGATCTCCCTCAGTCT GCCCCCAGCCCCCAAACTCCTCCTGGCTAGA FGF5 903 CCATTGACTTTGCCATCCGGGTAG 904 GCATCGGTTTCCATCTGCAGATCTACCCGGATGGCAAAGTCAA TGGATCCCACGAAGCCAATATGTT FGF6 907 CATCCACCTTGCCTCTCAGGCAC 908 GGGCCATTAATTCTGACCACGTGCCTGAGAGGCAAGGTGGAT GGCCCTGGGACAGAAACTGTTCATCACTATGTCCCGGG FGF7 911 CAGCCCTGAGCGACACACAAGAAG 912 CCAGAGCAAATGGCTACAAATGTGAACTGTTCCAGCCCTGAGC GACACACAAGAAGTTATGATTACATGGAAGGAGGGGA FGFR2 915 TCCCAGAGACCAACGTTCAAGCAGTTG 916 GAGGGACTGTTGGCATGCAGTGCCCTCCCAGAGACCAACGTT CAAGCAGTTGGTAGAAGACTTGGATCGAATTCTCACTC FGFR4 919 CCTTTCATGGGGAGAACCGCATT 920 CTGGCTTAAGGATGGACAGGCCTTTCATGGGGAGAACCGCAT TGGAGGCATTCGGCTGCGCCATCAGCACTGGAGTCTCGT FKBP5 923 TCTCCCCAGTTCCACAGCAGTGTC 924 CCCACAGTAGAGGGGTCTCATGTCTCCCCAGTTCCACAGCAG TGTCACAGACGTGAAAGCCAGAACC FLNA 927 TACCAGGCCCATAGCACTGGACAC 928 GAACCTGCGGTGGACACTTCCGGTGTCCAGTGCTATGGGCCT GGTATTGAGGGCCAGGGTGTCTTC FLNC 931 ATGTGCTGTCAGCTACCTGCCCAC 932 CAGGACAATGGTGATGGCTCATGTGCTGTCAGCTACCTGCCCA CGGAGCCTGGCGAGTACACCATCA FLT1 935 CTACAGCACCAAGAGCGACGTGTG 936 GGCTCCTGAATCTATCTTTGACAAAATCTACAGCACCAAGAGC GACGTGTGGTCTTACGGAGTATTGCTGTGGGA FLT4 939 AGCCCGCTGACCATGGAAGATCT 940 ACCAAGAAGCTGAGGACCTGTGGCTGAGCCCGCTGACCATGG AAGATCTTGTCTGCTACAGCTTCCAGG FN1 943 ACTCTCAGGCGGTGTCCACATGAT 944 GGAAGTGACAGACGTGAAGGTCACCATCATGTGGACACCGCC TGAGAGTGCAGTGACCGGCTACCGTGT FOS 947 TCCCAGCATCATCCAGGCCCAG 948 CGAGCCCTTTGATGACTTCCTGTTCCCAGCATCATCCAGGCCC AGTGGCTCTGAGACAGCCCGCTCC FOXO1 951 TATGAACCGCCTGACCCAAGTGAA 952 GTAAGCACCATGCCCCACACCTCGGGTATGAACCGCCTGACC CAAGTGAAGACACCTGTACAAGTGCCTCTGCCCC FOXP3 955 TGTTTCCATGGCTACCCCACAGGT 956 CTGTTTGCTGTCCGGAGGCACCTGTGGGGTAGCCATGGAAAC AGCACATTCCCAGAGTTCCTCCAC FOXQ1 959 TGATTTATGTCCCTTCCCTCCCCC 960 TGTTTTTGTCGCAACTTCCATTGATTTATGTCCCTTCCCTCCCC CCTAAGTACATCAGGGAACCTTTCCA FSD1 963 CGCACCAAACAAGTGCTGCACA 964 AGGCCTCCTGTCCTTCTACAATGCCCGCACCAAACAAGTGCTG CACACTTTCAAGACCAGGTTCACACA FYN 967 CTGAAGCACGACAAGCTGGTCCAG 968 GAAGCGCAGATCATGAAGAAGCTGAAGCACGACAAGCTGGTC CAGCTCTATGCAGTGGTGTCTGAGGAG G6PD 971 CCAGCCTCAGTGCCACTTGACATT 972 AATCTGCCTGTGGCCTTGCCCGCCAGCCTCAGTGCCACTTGA CATTCCTTGTCACCAGCAACATCTCG GABRG2 975 CTCAGCACCATTGCCCGGAAAT 976 CCACTGTCCTGACAATGACCACCCTCAGCACCATTGCCCGGA AATCGCTCCCCAAGGTCTCCTATGTCACAGCGATGGATCTC GADD45A 979 TTCATCTCAATGGAAGGATCCTGCC 980 GTGCTGGTGACGAATCCACATTCATCTCAATGGAAGGATCCTG CCTTAAGTCAACTTATTTGTTTTTGCCGGG GADD45B 983 TGGGAGTTCATGGGTACAGA 984 ACCCTCGACAAGACCACACTTTGGGACTTGGGAGCTGGGGCT GAAGTTGCTCTGTACCCATGAACTCCCA GDF15 987 TGTTAGCCAAAGACTGCCACTGCA 988 CGCTCCAGACCTATGATGACTTGTTAGCCAAAGACTGCCACTG CATATGAGCAGTCCTGGTCCTTCCACTGT GHR 991 CGTGCCTCAGCCTCCTGAGTAGCT 992 CCACCTCCCACAGGTTCAGGCGATTCCCGTGCCTCAGCCTCC TGAGTAGCTGGGACTACAGGCACGCACC GNPTAB 995 CCCTGCTCACATGCCTCACATGAT 996 GGATTCACATCGCGGAAAGTCCCTGCTCACATGCCTCACATGA TTGACCGGATTGTTATGCAAGAAC GNRH1 999 TCCTGTCCTTCACTGTCCTTGCCA 1000 AAGGGCTAAATCCAGGTGTGACGGTATCTAATGATGTCCTGTC CTTCACTGTCCTTGCCATCACCAGCCACAGAGATCCAG GPM6B 1003 CGCTGAGAAACCAAACACACCCAG 1004 ATGTGCTTGGAGTGGCCTGGCTGGGTGTGTTTGGTTTCTCAGC GGTGCCCGTGTTTATGTTCTACA GPNMB 1007 CAAACAGTGCCCTGATCTCCGTTG 1008 CAGCCTCGCCTTTAAGGATGGCAAACAGTGCCCTGATCTCCGT TGGCTGCTTGGCCATATTTGTCA GPR68 1011 CTCAGCACCGTGGTCATCTTCCTG 1012 CAAGGACCAGATCCAGCGGCTGGTGCTCAGCACCGTGGTCAT CTTCCTGGCCTGCTTCCTGCCCTACC GPS1 1015 CCTCCTGCTGGCTTCCTTTGATCA 1016 AGTACAAGCAGGCTGCCAAGTGCCTCCTGCTGGCTTCCTTTGA TCACTGTGACTTCCCTGAGCTGC GRB7 1019 CTCCCCACCCTTGAGAAGTGCCT 1020 CCATCTGCATCCATCTTGTTTGGGCTCCCCACCCTTGAGAAGT GCCTCAGATAATACCCTGGTGGCC GREM1 1023 TCCACCCTCCCTTTCTCACTCCAC 1024 GTGTGGGCAAGGACAAGCAGGATAGTGGAGTGAGAAAGGGAG GGTGGAGGGTGAGGCCAAATCAGGTC GSK3B 1027 CCAGGAGTTGCCACCACTGTTGTC 1028 GACAAGGACGGCAGCAAGGTGACAACAGTGGTGGCAACTCCT GGGCAGGGTCCAGACAGGCCACAA GSN 1031 ACCCAGCCAATCGGGATCGGC 1032 CTTCTGCTAAGCGGTACATCGAGACGGACCCAGCCAATCGGG ATCGGCGGACGCCCATCACCGTGGTGAAGCAAGGCTTTGAGC C GSTM1 1035 TCAGCCACTGGCTTCTGTCATAATCAGG 1036 AAGCTATGAGGAAAAGAAGTACACGATGGGGGACGCTCCTGA AG TTATGACAGAAGCCAGTGGCTGAATGAAAAATTCAAGCTGGGC C GSTM2 1039 CTGAAGCTCTACTCACAGTTTCTGGG 1040 CTGCAGGCACTCCCTGAAATGCTGAAGCTCTACTCACAGTTTC TGGGGAAGCAGCCATGGTTTCTTGG HDAC1 1043 TTCTTGCGCTCCATCCGTCCAGA 1044 CAAGTACCACAGCGATGACTACATTAAATTCTTGCGCTCCATC CGTCCAGATAACATGTCGGAGTACAGCAAGC HDAC9 1047 CCCCCTGAAGCTCTTCCTCTGCTT 1048 AACCAGGCAGTCACCTTGAGGAAGCAGAGGAAGAGCTTCAGG GGGACCAGGCGATGCAGGAAGACAGAG HGD 1051 CTGAGCAGCTCTCAGGATCGGCTT 1052 CTCAGGTCTGCCCCTACAATCTCTATGCTGAGCAGCTCTCAGG ATCGGCTTTCACTTGTCCACGGAGCACCAATAA HIP1 1055 CGACTCACTGACCGAGGCCTGTAA 1056 CTCAGAGCCCCACCTGAGCCTGCCGACTCACTGACCGAGGCC TGTAAGCAGTATGGCAGGGAAACCC HIRIP3 1059 CCATTGCTCCTGGTTCTGGGTTTC 1060 GGATGAGGAAAAGGGGGATTGGAAACCCAGAACCAGGAGCAA TGGCCGGAGAAAGTCAGCTAGGGA HK1 1063 TAAGAGTCCGGGATCCCCAGCCTA 1064 TACGCACAGAGGCAAGCAGCTAAGAGTCCGGGATCCCCAGCC TACTGCCTCTCCAGCACTTCTCTC HLA-G 1067 CTGCAAGGACAACCAGGCCAGCAA 1068 CCTGCGCGGCTACTACAACCAGAGCGAGGCCAGTTCTCACAC CCTCCAGTGGATGATTGGCTGCGACCTG HLF 1071 TAAGTGATCTGCCCTCCAGGTGGC 1072 CACCCTGCAGGTGTCTGAGACTAAGTGATCTGCCCTCCAGGT GGCGATCACCTTCTGCTCCTAGGTACC HNF1B 1075 CCCCTATGAAGACCCAGAAGCGTG 1076 TCCCAGCATCTCAACAAGGGCACCCCTATGAAGACCCAGAAG CGTGCCGCTCTGTACACCTGGTACG HPS1 1079 CAGTCACCAGCCCAAAGTGCACTT 1080 GCGGAAGCTGTATGTGCTCAAGTACCTGTTTGAAGTGCACTTT GGGCTGGTGACTGTGGACGGTCATCTTATCCGAA HRAS 1083 ACCACCTGCTTCCGGTAGGAATCC 1084 GGACGAATACGACCCCACTATAGAGGATTCCTACCGGAAGCA GGTGGTCATTGATGGGGAGACGTGC HSD17B10 1087 TCATGGGCACCTTCAATGTGATCC 1088 CCACCAGACAAGACCGATTCGCTGGCCTCCATTTCTTCAACCC AGTGCCTGTCATGAAACTTGTGG HSD17B2 1091 AGTTGCTTCCATCCAACCTGGAGG 1092 GCTTTCCAAGTGGGGAATTAAAGTTGCTTCCATCCAACCTGGA GGCTTCCTAACAAATATCGCAGGCA HSD17B3 1095 CTTCATCCTCACAGGGCTGCTGGT 1096 GGGACGTCCTGGAACAGTTCTTCATCCTCACAGGGCTGCTGG TGTGCCTGGCCTGCCTGGCGAAGTGCGTGAGATTCTCCA HSD17B4 1099 AGGCGGCGTCCTATTTCCTCAAAT 1100 CGGGAAGCTTCAGAGTACCTTTGTATTTGAGGAAATAGGACGC CGCCTAAAGGATATTGGGCCTGAGGT HSD3B2 1103 ACTTCCAGCAGGAAGCCAATCCAG 1104 GCCTTCCTTTAACCCTGATGTACTGGATTGGCTTCCTGCTGGA AGTAGTGAGCTTCCTACTCAGCCCAATTTACTCC HSP90AB1 1107 ATCCGCTCCATATTGGCTGTCCAG 1108 GCATTGTGACCAGCACCTACGGCTGGACAGCCAATATGGAGC GGATCATGAAAGCCCAGGCACTTC HSPA5 1111 TAATTAGACCTAGGCCTCAGCTGCACTG 1112 GGCTAGTAGAACTGGATCCCAACACCAAACTCTTAATTAGACC CC TAGGCCTCAGCTGCACTGCCCGAAAAGCATTTGGGCAGACC HSPA8 1115 CTCAGGGCCCACCATTGAAGAGGTTG 1116 CCTCCCTCTGGTGGTGCTTCCTCAGGGCCCACCATTGAAGAG GTTGATTAAGCCAACCAAGTGTAGATGTAGC HSPB1 1119 CGCACTTTTCTGAGCAGACGTCCA 1120 CCGACTGGAGGAGCATAAAAGCGCAGCCGAGCCCAGCGCCC CGCACTTTTCTGAGCAGACGTCCAGAGCAGAGTCAGCCAGCA T HSPB2 1123 CACCTTTCCCTTCCCCCAAGGAT 1124 CACCACTCCAGAGGTAGCAGCATCCTTGGGGGAAGGGAAAGG TGCATGGTCCACAATGTATGGTTTGGTCCCA HSPE1 1127 TCTCCACCCTTTCCTTTAGAACCCG 1128 GCAAGCAACAGTAGTCGCTGTTGGATCGGGTTCTAAAGGAAA GGGTGGAGAGATTCAACCAGTTAGCGTGAAAGTTGG HSPG2 1131 CAGCTCCGTGCCTCTAGAGGCCT 1132 GAGTACGTGTGCCGAGTGTTGGGCAGCTCCGTGCCTCTAGAG GCCTCTGTCCTGGTCACCATTGAG ICAM1 1135 CCGGCGCCCAACGTGATTCT 1136 GCAGACAGTGACCATCTACAGCTTTCCGGCGCCCAACGTGATT CTGACGAAGCCAGAGGTCTCAGAAG IER3 1139 TCAAGTTGCCTCGGAAGTCCCAGT 1140 GTACCTGGTGCGCGAGAGCGTATCCCCAACTGGGACTTCCGA GGCAACTTGAACTCAGAACACTACAGCGGAGACGC IFI30 1143 AAAATTCCACCCCATGATCAAGAATCC 1144 ATCCCATGAAGCCCAGATACACAAAATTCCACCCCATGATCAA GAATCCTGCTCCACTAAGAATGGTGC IFIT1 1147 AAGTTGCCCCAGGTCACCAGACTC 1148 TGACAACCAAGCAAATGTGAGGAGTCTGGTGACCTGGGGCAA CTTTGCCTGGATGTATTACCACATGGGCAGACTG IFNG 1151 TCGACCTCGAAACAGCATCTGACTCC 1152 GCTAAAACAGGGAAGCGAAAAAGGAGTCAGATGCTGTTTCGA GGTCGAAGAGCATCCCAGTAATGGTTG IGF1 1155 TGTATTGCGCACCCCTCAAGCCTG 1156 TCCGGAGCTGTGATCTAAGGAGGCTGGAGATGTATTGCGCAC CCCTCAAGCCTGCCAAGTCAGCTCGCTCTGTCCG IGF1R 1159 CGCGTCATACCAAAATCTCCGATTTTGA 1160 GCATGGTAGCCGAAGATTTCACAGTCAAAATCGGAGATTTTGG TATGACGCGAGATATCTATGAGACAGACTATTACCGGAAA IGF2 1163 TACCCCGTGGGCAAGTTCTTCCAA 1164 CCGTGCTTCCGGACAACTTCCCCAGATACCCCGTGGGCAAGT TCTTCCAATATGACACCTGGAAGCAGTCCA IGFBP2 1167 CTTCCGGCCAGCACTGCCTC 1168 GTGGACAGCACCATGAACATGTTGGGCGGGGGAGGCAGTGCT GGCCGGAAGCCCCTCAAGTCGGGTATGAAGG IGFBP3 1171 ACACCACAGAAGGCTGTGAGCTCC 1172 ACATCCCAACGCATGCTCCTGGAGCTCACAGCCTTCTGTGGTG TCATTTCTGAAACAAGGGCGTGG IGFBP5 1175 CCCGTCAACGTACTCCATGCCTGG 1176 TGGACAAGTACGGGATGAAGCTGCCAGGCATGGAGTACGTTG ACGGGGACTTTCAGTGCCACACCTTCG IGKBP6 1179 ATCCAGGCACCTCTACCACGCCCTC 1180 TGAACCGCAGAGACCAACAGAGGAATCCAGGCACCTCTACCA CGCCCTCCCAGCCCAATTCTGCGGGTGTCCAAGAC IL10 1183 TTGAGCTGTTTTCCCTGACCTCCC 1184 CTGACCACGCTTTCTAGCTGTTGAGCTGTTTTCCCTGACCTCC CTCTAATTTATCTTGTCTCTGGGCTTGG IL11 1187 CCTGTGATCAACAGTACCCGTATGGG 1188 TGGAAGGTTCCACAAGTCACCCTGTGATCAACAGTACCCGTAT GGGACAAAGCTGCAAGGTCAAGA IL17A 1191 TGGCTTCTGTCTGATCAAGGCACC 1192 TCAAGCAACACTCCTAGGGCCTGGCTTCTGTCTGATCAAGGCA CCACACAACCCAGAAAGGAGCTG IL1A 1195 TCTCCACCCTGGCCCTGTTACAGT 1196 GGTCCTTGGTAGAGGGCTACTTTACTGTAACAGGGCCAGGGT GGAGAGTTCTCTCCTGAAGCTCCATCC IL1B 1199 TGCCCACAGACCTTCCAGGAGAAT 1200 AGCTGAGGAAGATGCTGGTTCCCTGCCCACAGACCTTCCAGG AGAATGACCTGAGCACCTTCTTTCC IL2 1203 TGCAACTCCTGTCTTGCATTGCAC 1204 ACCTCAACTCCTGCCACAATGTACAGGATGCAACTCCTGTCTT GCATTGCACTAAGTCTTGCACTTGTCACAAACAGTG IL6 1207 CCAGATTGGAAGCATCCATCTTTTTCA 1208 CCTGAACCTTCCAAAGATGGCTGAAAAAGATGGATGCTTCCAA TCTGGATTCAATGAGGAGACTTGCCTGGT IL6R 1211 CCTTTGGCTTCACGGAAGAGCCTT 1212 CCAGCTTATCTCAGGGGTGTGCGGCCTTTGGCTTCACGGAAG AGCCTTGCGGAAGGTTCTACGCCAG IL6ST 1215 CATATTGCCCAGTGGTCACCTCACA 1216 GGCCTAATGTTCCAGATCCTTCAAAGAGTCATATTGCCCAGTG GTCACCTCACACTCCTCCAAGGCACAATTTT IL8 1219 TGACTTCCAAGCTGGCCGTGGC 1220 AAGGAACCATCTCACTGTGTGTAAACATGACTTCCAAGCTGGC CGTGGCTCTCTTGGCAGCCTTCCTGAT ILF3 1223 ACACAAGACTTCAGCCCGTTGGCT 1224 GACACGCCAAGTGGTTCCAGGCCAGAGCCAACGGGCTGAAGT CTTGTGTCATTGTGATCCGGGTCTTGAG ILK 1227 ATGTGCTCCCAGTGCTAGGTGCCT 1228 CTCAGGATTTTCTCGCATCCAAATGTGCTCCCAGTGCTAGGTG CCTGCCAGTCTCCACCTGCTCCT IMMT 1231 CAACTGCATGGCTCTGAACAGCCT 1232 CTGCCTATGCCAGACTCAGAGGAATCGAACAGGCTGTTCAGA GCCATGCAGTTGCTGAAGAGGAAGCCAGAAAAGC ING5 1235 CCAGCTGCACTTTGTCGTCACTGT 1236 CCTACAGCAAGTGCAAGGAATACAGTGACGACAAAGTGCAGC TGGCCATGCAGACCTACGAGATG INHBA 1239 ACGTCCGGGTCCTCACTGTCCTTCC 1240 GTGCCCGAGCCATATAGCAGGCACGTCCGGGTCCTCACTGTC CTTCCACTCAACAGTCATCAACCACTACCG INSL4 1243 TGAGAAGACATTCACCACCACCCC 1244 CTGTCATATTGCCCCATGCCTGAGAAGACATTCACCACCACCC CAGGAGGGTGGCTGCTGGAATCTG ITGA1 1247 TTGCTGGACAGCCTCGGTACAATC 1248 GCTTCTTCTGGAGATGTGCTCTATATTGCTGGACAGCCTCGGT ACAATCATACAGGCCAGGTCATTATCTACAGG ITGA3 1251 CACTCCAGACCTCGCTTAGCATGG 1252 CCATGATCCTCACTCTGCTGGTGGACTATACACTCCAGACCTC GCTTAGCATGGTAAATCACCGGCTACAAAGCTTC ITGA4 1255 CGATCCTGCATCTGTAAATCGCCC 1256 CAACGCTTCAGTGATCAATCCCGGGGCGATTTACAGATGCAG GATCGGAAAGAATCCCGGCCAGAC ITGA5 1259 TCTGAGCCTTGTCCTCTATCCGGC 1260 AGGCCAGCCCTACATTATCAGAGCAAGAGCCGGATAGAGGAC AAGGCTCAGATCTTGCTGGACTGTGGAGAAGAC ITGA6 1263 TCGCCATCTTTTGTGGGATTCCTT 1264 CAGTGACAAACAGCCCTTCCAACCCAAGGAATCCCACAAAAGA TGGCGATGACGCCCATGAGGCTAAAC ITGA7 1267 CAGCCAGGACCTGGCCATCCG 1268 GATATGATTGGTCGCTGCTTTGTGCTCAGCCAGGACCTGGCCA TCCGGGATGAGTTGGATGGTGGGGAATGGAAGTTCT ITGAD 1271 CAACTGAAAGGCCTGACGTTCACG 1272 GAGCCTGGTGGATCCCATCGTCCAACTGAAAGGCCTGACGTT CACGGCCACGGGCATCCTGACAGT ITGB3 1275 AAATACCTGCAACCGTTACTGCCGTGAC 1276 ACCGGGGAGCCCTACATGACGAAAATACCTGCAACCGTTACT GCCGTGACGAGATTGAGTCAGTGAAAGAGCTTAAGG ITGB4 1279 CACCAACCTGTACCCGTATTGCGA 1280 CAAGGTGCCCTCAGTGGAGCTCACCAACCTGTACCCGTATTG CGACTATGAGATGAAGGTGTGCGC ITGB5 1283 TGCTATGTTTCTACAAAACCGCCAAGG 1284 TCGTGAAAGATGACCAGGAGGCTGTGCTATGTTTCTACAAAAC CGCCAAGGACTGCGTCATGATGTTCACC ITPR1 1287 CCATCCTAACGGAACGAGCTCCCT 1288 GAGGAGGTGTGGGTGTTCCGCTTCCATCCTAACGGAACGAGC TCCCTCTTCGCGGACATGGGATTAC ITPR3 1291 TCCAGGTCTCGGATCTCAGACACG 1292 TTGCCATCGTGTCAGTGCCCGTGTCTGAGATCCGAGACCTGG ACTTTGCCAATGACGCCAGCTCCAT ITSN1 1295 AGCCCTCTCTCACCGTTCCAAGTG 1296 TAACTGGGATGCATGGGCAGCCCAGCCCTCTCTCACCGTTCC AAGTGCCGGCCAGTTAAGGCAGAG JAG1 1299 ACTCGATTTCCCAGCCAACCACAG 1300 TGGCTTACACTGGCAATGGTAGTTTCTGTGGTTGGCTGGGAAA TCGAGTGCCGCATCTCACAGCTATGC JUN 1303 CTATGACGATGCCCTCAACGCCTC 1304 GACTGCAAAGATGGAAACGACCTTCTATGACGATGCCCTCAAC GCCTCGTTCCTCCCGTCCGAGAGCGGACCTTATGGCTA JUNB 1307 CAAGGGACACGCCTTCTGAACGT 1308 CTGTCAGCTGCTGCTTGGGGTCAAGGGACACGCCTTCTGAAC GTCCCCTGCCCCTTTACGGACACCCCCT KCNN2 1311 TTATACATTCACATGGACGGCCCG 1312 TGTGCTATTCATCCCATACCTGGGAATTATACATTCACATGGAC GGCCCGGCTTGCCTTCTCCTATGCCC KCTD12 1315 ACTCTTAGGCGGCAGCGTCCTTTC 1316 AGCAGTTACTGGCAAGAGGGAGAAAGGACGCTGCCGCCTAAG AGTGCAAGGCTGCTCAGGTCTCCA KNDRBS3 1319 CAAGACACAAGGCACCTTCAGCGA 1320 CGGGCAAGAAGAGTGGACTAACTCAAGACACAAGGCACCTTC AGCGAGGACAGCAAAGGGCGTCTACAG KIAA0196 1323 TCCCCAGTGTCCAGGCACAGAGTA 1324 CAGACACCAGCTCTGAGGCCAGTTAATCATCCCCAGTGTCCAG GCACAGAGTAGTCGGTCCGCCTCACAATGTT KIAA0247 1327 TCCGCTAGTGATCCTTTGCACCCT 1328 CCGTGGGACATGGAGTGTTCCTTCCGCTAGTGATCCTTTGCAC CCTGCTTGGAGACGGACTTGCTTC KF4A 1331 CAGGTCAGCAAACTTGAAAGCAGCC 1332 AGAGCTGGTCTCCTCCAAAATACAGGTCAGCAAACTTGAAAGC AGCCTGAAACAGAGCAAGACCAGC KIT 1335 TTACAGCGACAGTCATGGCCGCAT 1336 GAGGCAACTGCTTATGGCTTAATTAAGTCAGATGCGGCCATGA CTGTCGCTGTAAAGATGCTCAAGCCGAGTGCC KLC1 1339 CAACACGCAGCAGAAACTGCAGAA 1340 AGTGGCTACGGGATGAACTGGCCAACACGCAGCAGAAACTGC AGAAGAGTGAGCAGTCTGTGGCTCA KLF6 1343 AGTACTCCTCCAGAGACGGCAGCG 1344 CACGAGACCGGCTACTTCTCGGCGCTGCCGTCTCTGGAGGAG TACTGGCAACAGACCTGCCTAGAGC KLK1 1347 TCAGTGAGAGCTTCCCACACCCTG 1348 AACACAGCCCAGTTTGTTCATGTCAGTGAGAGCTTCCCACACC CTGGCTTCAACATGAGCCTCCTGG KLK10 1351 CCTCTTCCTCCCCAGTCGGCTGA 1352 GCCCAGAGGCTCCATCGTCCATCCTCTTCCTCCCCAGTCGGCT GAACTCTCCCCTTGTCTGCACTGTTCAAACCTCTG KLK11 1355 CCTCCCCAACAAAGACCACCGCA 1356 CACCCCGGCTTCAACAACAGCCTCCCCAACAAAGACCACCGC AATGACATCATGCTGGTGAAGATG KLK14 1359 CAGCACTTCAAGTCCTGGCTATAGCCA 1360 CCCCTAAAATGTTCCTCCTGCTGACAGCACTTCAAGTCCTGGC TATAGCCATGACACAGAGCCAAGAGGATGAG KLK2 1363 TTGGGAATGCTTCTCACACTCCCA 1364 AGTCTCGGATTGTGGGAGGCTGGGAGTGTGAGAAGCATTCCC AACCCTGGCAGGTGGCTGTGTACA KLK3 1367 ACCCACATGGTGACACAGCTCTCC 1368 CCAAGCTTACCACCTGCACCCGGAGAGCTGTGTCACCATGTG GGTCCCGGTTGTCTTCCTCACCCT KLRK1 1371 TGTCTCAAAATGCCAGCCTTCTGAA 1372 TGAGAGCCAGGCTTCTTGTATGTCTCAAAATGCCAGCCTTCTG AAAGTATACAGCAAAGAGGACCAGGAT KPNA2 1375 ACTCCTGTTTTCACCACCATGCCA 1376 TGATGGTCCAAATGAACGAATTGGCATGGTGGTGAAAACAGGA GTTGTGCCCCAACTTGTGAAGCTT KRT1 1379 CCTCAGCAATGATGCTGTCCAGGT 1380 TGGACAACAACCGCAGTCTCGACCTGGACAGCATCATTGCTGA GGTCAAGGCCCAGTACGAGGATA KRT15 1383 TGAACAAAGAGGTGGCCTCCAACA 1384 GCCTGGTTCTTCAGCAAGACTGAGGAGCTGAACAAAGAGGTG GCCTCCAACACAGAAATGATCCAGACCAGCAAG KRT18 1387 TGGTTCTTCTTCATGAAGAGCAGCTCC 1388 AGAGATCGAGGCTCTCAAGGAGGAGCTGCTCTTCATGAAGAA GAACCACGAAGAGGAAGTAAAAGGCC KRT2 1391 ACCTAGACAGCACAGATTCCGCCC 1392 CCAGTGACGCCTCTGTGTTCTGGGGCGGAATCTGTGCTGTCTA GGTTTGTGCTTCTAGCCATGCCC KRT5 1395 CCAGTCAACATCTCTGTTGTCACAAGCA 1396 TCAGTGGAGAAGGAGTTGGACCAGTCAACATCTCTGTTGTCAC AAGCAGTGTTTCCTCTGGATATGGCA KRT75 1399 TTCATTCTCAGCAGCTGTGCGCTTGT 1400 TCAAAGTCAGGTACGAAGATGAAATTAACAAGCGCACAGCTGC TGAGAATGAATTTGTAGCCCTGAAAAAGGACGT KRT76 1403 TCTGGGCTTCAGATCCTGACTCCC 1404 ATCTCCAGACTGCTGGTTCCCAGGGAACCCTCCCTACATCTGG GCTTCAGATCCTGACTCCCTTCTGTCCCCTAATTCCCTGA KRT8 1407 CGTCGGTCAGCCCTTCCAGGC 1408 GGATGAAGCTTACATGAACAAGGTAGAGCTGGAGTCTCGCCT GGAAGGGCTGACCGACGAGATCAACTTCCTCAGGCAGCTATA TG L1CAM 1411 ATCTACGTTGTCCAGCTGCCAGCC 1412 CTTGCTGGCCAATGCCTACATCTACGTTGTCCAGCTGCCAGCC AAGATCCTGACTGCGGACAATCA LAG3 1415 TCTATCTTGCTCTGAGCCTGCGGA 1416 GCCTTAGAGCAAGGGATTCACCCTCCGCAGGCTCAGAGCAAG ATAGAGGAGCTGGAGCAAGAACCG LAMA3 1419 ATTCAGACTGACAGGCCCCTGGAC 1420 CCTGTCACTGAAGCCTTGGAAGTCCAGGGGCCTGTCAGTCTG AATGGTTGTCCTGACCAGTAACCCA LAMA4 1423 CTCTCCATCGAGGAAGGCAAATCC 1424 GATGCACTGCGGTTAGCAGCGCTCTCCATCGAGGAAGGCAAA TCCGGGGTGCTGAGCGTATCCTCTG LAMA5 1427 CTGTTCCTGGAGCATGGCCTCTTC 1428 CTCCTGGCCAACAGCACTGCACTAGAAGAGGCCATGCTCCAG GAACAGCAGAGGCTGGGCCTTGTGT LAMB1 1431 CAAGTGCCTGTACCACACGGAAGG 1432 CAAGGAGACTGGGAGGTGTCTCAAGTGCCTGTACCACACGGA AGGGGAACACTGTCAGTTCTGCCG LAMB3 1435 CCACTCGCCATACTGGGTGCAGT 1436 ACTGACCAAGCCTGAGACCTACTGCACCCAGTATGGCGAGTG GCAGATGAAATGCTGCAAGTGTGAC LAMC1 1439 CCTCGGTACTTCATTGCTCCTGCA 1440 GCCGTGATCTCAGACAGCTACTTTCCTCGGTACTTCATTGCTC CTGCAAAGTTCTTGGGCAAGCAGGT LAMC2 1443 AGGTCTTATCAGCACAGTCTCCGCCTCC 1444 ACTCAAGCGGAAATTGAAGCAGATAGGTCTTATCAGCACAGTC TCCGCCTCCTGGATTCAGTGTCTCGGCTTCAGGGAGT LAPTM5 1447 TCCTGACCCTCTGCAGCTCCTACA 1448 TGCTGGACTTCTGCCTGAGCATCCTGACCCTCTGCAGCTCCTA CATGGAAGTGCCCACCTATCTCA LGALS3 1451 ACCCAGATAACGCATCATGGAGCGA 1452 AGCGGAAAATGGCAGACAATTTTTCGCTCCATGATGCGTTATC TGGGTCTGGAAACCCAAACCCTCAAG LIG3 1455 CTGGACGCTCAGAGCTCGTCTCTG 1456 GGAGGTGGAGAAGGAGCCGGGCCAGAGACGAGCTCTGAGCG TCCAGGCCTCGCTGATGACACCTGT LIMS1 1459 ACTGAGCGCACACGAAACACTGCT 1460 TGAACAGTAATGGGGAGCTGTACCATGAGCAGTGTTTCGTGTG CGCTCAGTGCTTCCAGCAGTTCCCAGAA LOX 1463 CAGGCTCAGCAAGCTGAACACCTG 1464 CCAATGGGAGAACAACGGGCAGGTGTTCAGCTTGCTGAGCCT GGGCTCACAGTACCAGCCTCAGCG LRP1 1467 TCCCGGCTGGGCGCCTCTACT 1468 TTTGGCCCAATGGGCTAAGCCTGGACATCCCGGCTGGGCGCC TCTACTGGGTGGATGCCTTCTACGACCGCATCGAGAC LTBP2 1471 CTTTGCAGCCCTCAGAACTCCAGC 1472 GCACACCCATCCTTGAGTCTCCTTTGCAGCCCTCAGAACTCCA GCCCCACTACGTGGCCAGCCATC LUM 1475 CCTGACCTTCATCCATCTCCAGCA 1476 GGCTCTTTTGAAGGATTGGTAAACCTGACCTTCATCCATCTCC AGCACAATCGGCTGAAAGAGGATGCTGTTTCAGCTGCTTTT MAGEA4 1479 CAGCTTCCCTTGCCTCGTGTAACA 1480 GCATCTAACAGCCCTGTGCAGCAGCTTCCCTTGCCTCGTGTAA CATGAGGCCCATTCTTCACTCTG MANF 1483 TTCCTGATGATGCTGGCCCTACAG 1484 CAGATGTGAAGCCTGGAGCTTTCCTGATGATGCTGGCCCTACA GTACCCCCATGAGGGGATTCCCTT MAOA 1487 CCGCGATACTCGCCTTCTCTTGAT 1488 GTGTCAGCCAAAGCATGGAGAATCAAGAGAAGGCGAGTATCG CGGGCCACATGTTCGACGTAGTCG MAP3K5 1491 CAGCCCAGAGACCAGATGTCTGCT 1492 AGGACCAAGAGGCTACGGAAAAGCAGCAGACATCTGGTCTCT GGGCTGTACAATCATTGAAATGGCCACAGG MAP3K7 1495 TGCTGGTCCTTTTCATCCTGGTCC 1496 CAGGCAAGAACTAGTTGCAGAACTGGACCAGGATGAAAAGGA CCAGCAAAATACATCTCGCCTGGTACAGG MAP4K4 1499 AACGTTCCTTGTTCTCCTGCTGCA 1500 TCGCCGAGATTTCCTGAGACTGCAGCAGGAGAACAAGGAACG TTCCGAGGCTCTTCGGAGACAACAG MAP7 1503 CATGTACAACAAACGCTCCGGGAA 1504 GAGGAACAGAGGTGTCTGCACTTCCATGTACAACAAACGCTCC GGGAAATGGAAAGCCAGTTGGCAG MAPKAPK3 1507 ATTGGCACTGCCATCCAGTTTCTG 1508 AAGCTGCAGAGATAATGCGGGATATTGGCACTGCCATCCAGTT TCTGCACAGCCATAACATTGCCCAC MCM2 1511 ACAGCTCATTGTTGTCACGCCGGA 1512 GACTTTTGCCCGCTACCTTTCATTCCGGCGTGACAACAATGAG CTGTTGCTCTTCATACTGAAGCAGTTAGTGGC MCM3 1515 TGGCCTTTCTGTCTACAAGGATCACCA 1516 GGAGAACAATCCCCTTGAGACAGAATATGGCCTTTCTGTCTAC AAGGATCACCAGACCATCACCATCCAGGAGAT MCM6 1519 CAGGTTTCATACCAACACAGGCTTCAGC 1520 TGATGGTCCTATGTGTCACATTCATCACAGGTTTCATACCAACA AC CAGGCTTCAGCACTTCCTTTGGTGTGTTTCCTGTCCCA MDK 1523 ATCACACGCACCCCAGTTCTCAAA 1524 GGAGCCGACTGCAAGTACAAGTTTGAGAACTGGGGTGCGTGT GATGGGGGCACAGGCACCAAAGTC MDM2 1527 CTTACACCAGCATCAAGATCCGG 1528 CTACAGGGACGCCATCGAATCCGGATCTTGATGCTGGTGTAAG TGAACATTCAGGTGATTGGTTGGAT MELK 1531 CCCGGGTTGTCTTCCGTCAGATAG 1532 AGGATCGCCTGTCAGAAGAGGAGACCCGGGTTGTCTTCCGTC AGATAGTATCTGCTGTTGCTTATGTGCA MET 1535 TGCCTCTCTGCCCCACCCTTTGT 1536 GACATTTCCAGTCCTGCAGTCAATGCCTCTCTGCCCCACCCTT TGTTCAGTGTGGCTGGTGCCACGACAAATGTGTGCGATCGGA G MGMT 1539 CAGCCCTTTGGGGAAGCTGG 1540 GTGAAATGAAACGCACCACACTGGACAGCCCTTTGGGGAAGC TGGAGCTGTCTGGTTGTGAGCAGGGTC MGST1 1543 TTTGACACCCCTTCCCCAGCCA 1544 ACGGATCTACCACACCATTGCATATTTGACACCCCTTCCCCAG CCAAATAGAGCTTTGAGTTTTTTTGTTGGATATGGA MICA 1547 CGAGGCCTCAGAGGGCAACATTAC 1548 ATGGTGAATGTCACCCGCAGCGAGGCCTCAGAGGGCAACATT ACCGTGACATGCAGGGCTTCTGGCTT MKI67 1551 CCACTCTTCCTTGAACACCCTCCC 1552 GATTGCACCAGGGCAGAACAGGGGAGGGTGTTCAAGGAAGAG TGGCTCTTAGCAGAGGCACTTTGGA MLXIP 1555 CATGAGATGCCAGGAGACCCTTCC 1556 TGCTTAGCTGGCATGTGGCCGCATGAGATGCCAGGAGACCCT TCCCTGCCCATGGAGAGTAGGCTG MMP11 1559 ATCCTCCTGAAGCCCTTTTCGCAGC 1560 CCTGGAGGCTGCAACATACCTCAATCCTGTCCCAGGCCGGAT CCTCCTGAAGCCCTTTTCGCAGCACTGCTATCCTCCAAAGCCA TTGTA MMP2 1563 AAGTCCGAATCTCTGCTCCCTGCA 1564 CAGCCAGAAGCGGAAACTTAAAAAGTCCGAATCTCTGCTCCCT GCAGGGCACAGGTGATGGTGTCT MMP7 1567 CCTGTATGCTGCAACTCATGAACTTGGC 1568 GGATGGTAGCAGTCTAGGGATTAACTTCCTGTATGCTGCAACT CATGAACTTGGCCATTCTTTGGGTATGGGACATTCC MMP9 1571 ACAGGTATTCCTCTGCCAGCTGCC 1572 GAGAACCAATCTCACCGACAGGCAGCTGGCAGAGGAATACCT GTACCGCTATGGTTACACTCGGGTG MPPED2 1575 ATTTGACCTTCCAAACCCACAGGG 1576 CCGACCAACCCTCCAATTATATTTGACCTTCCAAACCCACAGG GTTCCTGAAGCTCTAAATGCCCT MRC1 1579 CCAACCGCTGTTGAAGCTCAGACT 1580 CTTGACCTCAGGACTCTGGATTGGACTTAACAGTCTGAGCTTC AACAGCGGTTGGCAGTGGAGTGACCGCAGTCC MRPL13 1583 CGGCTGGAAATTATGTCCTCCGTC 1584 TCCGGTTCCCTTCGTTTAGGTCGGCTGGAAATTATGTCCTCCG TCGGTTTTCCGCAGTTTTTCCAC MSH2 1587 CAAGAAGATTTACTTCGTCGATTCCCAGA 1588 GATGCAGAATTGAGGCAGACTTTACAAGAAGATTTACTTCGTC GATTCCCAGATCTTAACCGACTTGCCAAGA MSH3 1591 TCCCAATTGTCGCTTCTTCTGCAG 1592 TGATTACCATCATGGCTCAGATTGGCTCCTATGTTCCTGCAGA AGAAGCGACAATTGGGATTGTGGATGGCATTTTCACAAG MSH6 1595 CCGTTACCAGCTGGAAATTCCTGAGA 1596 TCTATTGGGGGATTGGTAGGAACCGTTACCAGCTGGAAATTCC TGAGAATTTCACCACTCGCAATTTG MTA1 1599 CCCAGTGTCCGCCAAGGAGCG 1600 CCGCCCTCACCTGCAGAGAAACGCGCTCCTTGGCGGACACTG GGGGAGGAGAGGAAGAAGCGCGGCTAACTTATTCC MTPN 1603 AAGCTGCCCACAATCTGCTGCATA 1604 GGTGGAAGGAAACCTCTTCATTATGCAGCAGATTGTGGGCAGC TTGAAATCCTGGAATTTCTGCTGCTG MTSS1 1607 CCAAGAAACAGCGACATCAGCCAG 1608 TTCGACAAGTCCTCCACCATTCCAAGAAACAGCGACATCAGCC AGTCCTACCGACGGATGTTCCAAG MUC1 1611 CTCTGGCCTTCCGAGAAGGTACC 1612 GGCCAGGATCTGTGGTGGTACAATTGACTCTGGCCTTCCGAG AAGGTACCATCAATGTCCACGACGTGGAG MVP 1615 CGCACCTTTCCGGTCTTGACATCCT 1616 ACGAGAACGAGGGCATCTATGTGCAGGATGTCAAGACCGGAA AGGTGCGCGCTGTGATTGGAAGCACCTACATGC MYBL2 1619 CAGCATTGTCTGTCCTCCCTGGCA 1620 GCCGAGATCGCCAAGATGTTGCCAGGGAGGACAGACAATGCT GTGAAGAATCACTGGAACTCTACCATCAAAAG MYBPC1 1623 AAATTCGCAAGCCCAGCCCCTAT 1624 CAGCAACCAGGGAGTCTGTACCCTGGAAATTCGCAAGCCCAG CCCCTATGATGGAGGCACTTACTGCTG MYC 1627 TCTGACACTGTCCAACTTGACCCTCTT 1628 TCCCTCCACTCGGAAGGACTATCCTGCTGCCAAGAGGGTCAA GTTGGACAGTGTCAGAGTCCTGAGACAGATCAGCAACAACCG MYLK3 1631 CACACCCTCACAGATCTGCCTGGT 1632 CACCTGACTGAGCTGGATGTGGTCCTGTTCACCAGGCAGATCT GTGAGGGTGTGCATTACCTGCACCAGCACTACATC MYO6 1635 CAATCCTCAGGGCCAGCTCCC 1636 AAGCAGTTCTGGAGCAGGAGCGCAGGGACCGGGAGCTGGCC CTGAGGATTGCCCAGAGTGAAGCCGAGCTCATC NCAM1 1639 CTCAGCCTCGTCGTTCTTATCCACC 1640 TAGTTCCCAGCTGACCATCAAAAAGGTGGATAAGAACGACGAG GCTGAGTACATCTGCATTGCTGAGAACAAGGCTG NCAPD3 1643 CTACTGTCCGCAGCAAGGCACTGT 1644 TCGTTGCTTAGACAAGGCGCCTACTGTCCGCAGCAAGGCACT GTCCAGCTTTGCACACTGTCTGGAG NCOR1 1647 CCAGGCTCAGTCTGTCCATCATCA 1648 AACCGTTACAGCCCAGAATCCCAGGCTCAGTCTGTCCATCATC AAAGACCAGGTTCAAGGGTCTCTCCAGA NCOR2 1651 CCTCATAGGACAAGACGTGGCCCT 1652 CGTCATCTACGAAGGCAAGAAGGGCCACGTCTTGTCCTATGA GGGTGGCATGTCTGTGACCCAGTGCTC NDRG1 1655 CTGCAAGGACACTCATCACAGCCA 1656 AGGGCAACATTCCACAGCTGCCCTGGCTGTGATGAGTGTCCTT GCAGGGGCCGGAGTAGGAGCACTG NDUFS5 1659 TGTCCAAGAAAGGCATGGCTACCC 1660 AGAAGAGTCAAGGGCACGAGCATCGGGTAGCCATGCCTTTCT TGGACATCCAGAAAAGGTTCGGCCT NEK2 1663 TGCCTTCCCGGGCTGAGGACT 1664 GTGAGGCAGCGCGACTCTGGCGACTGGCCGGCCATGCCTTCC CGGGCTGAGGACTATGAAGTGTTGTACACCATTGGCA NETO2 1667 AGCCAACCCTTTTCTCCCATCACA 1668 CCAGGGCACCATACTGTTTCCAGCAGCCAACCCTTTTCTCCCA TCACAACTACGAAGACCTTGATTTACCGTT NEXN 1671 TCATCTTCAGCAGTGGAGCCATTCA 1672 AGGAGGAGGAAGAAGGTAGCATCATGAATGGCTCCACTGCTG AAGATGAAGAGCAAACCAGATCAGGAGCTC NFAT5 1675 CGAGAATCAGTCCCCGTGGAGTTC 1676 CTGAACCCCTCTCCTGGTCACCGAGAATCAGTCCCCGTGGAG TTCCCCCTCCACCTCGCCATCGTTTCCT NFATC2 1679 CGGGTTCCTACCCCACAGTCATTC 1680 CAGTCAAGGTCAGAGGCTGAGCCCGGGTTCCTACCCCACAGT CATTCAGCAGCAGAATGCCACGAGCCAAAG NFKB1 1683 AAGCTGTAAACATGAGCCGCACCA 1684 CAGACCAAGGAGATGGACCTCAGCGTGGTGCGGCTCATGTTT ACAGCTTTTCTTCCGGATAGCACTGGCAGCT NFKBIA 1687 CTCGTCTTTCATGGAGTCCAGGCC 1688 CTACTGGACGACCGCCACGACAGCGGCCTGGACTCCATGAAA GACGAGGAGTACGAGCAGATGGTCAAGG NME1 1691 CCTGGGACCATCCGTGGAGACTTCT 1692 CCAACCCTGCAGACTCCAAGCCTGGGACCATCCGTGGAGACT TCTGCATACAAGTTGGCAGGAACATTATACAT NNMT 1695 CCCTCTCCTCATGCCCAGACTCTC 1696 CCTAGGGCAGGGATGGAGAGAGAGTCTGGGCATGAGGAGAG GGTCTCGGGATGTTTGGCTGGACTAG NOS3 1699 TTCACTCGCTTCGCCATCACCG 1700 ATCTCCGCCTCGCTCATGGGCACGGTGATGGCGAAGCGAGTG AAGGCGACAATCCTGTATGGCTCCGA NOX4 1703 CCGAACACTCTTGGCTTACCTCCG 1704 CCTCAACTGCAGCCTTATCCTTTTACCCATGTGCCGAACACTC TTGGCTTACCTCCGAGGATCACAGAAGGTTCCAAGCA NPBWR1 1707 ATCGCCGACGAGCTCTTCACG 1708 TCACCAACCTGTTCATCCTCAACCTGGCCATCGCCGACGAGCT CTTCACGCTGGTGCTGCCCATCAACATC NPM1 1711 AACAGGCATTTTGGACAACACATTCTTG 1712 AATGTTGTCCAGGTTCTATTGCCAAGAATGTGTTGTCCAAAATG CCTGTTTAGTTTTTAAAGATGGAACTCCACCCTTTGCTTG NRG1 1715 ATGACCACCCCGGCTCGTATGTCA 1716 CGAGACTCTCCTCATAGTGAAAGGTATGTGTCAGCCATGACCA CCCCGGCTCGTATGTCACCTGTAGATTTCCACACGCCAAG NRIP3 1719 AGCTTTCTCTACCCCGGCATCTCA 1720 CCCACAAGCATGAAGGAGAAAAGCTTTCTCTACCCCGGCATCT CAAAGTAGTGGGCCAGATTGAGCA NRP1 1723 CAGGATCTACCCCGAGAGAGCCACTCAT 1724 CAGCTCTCTCCACGCGATTCATCAGGATCTACCCCGAGAGAG CCACTCATGGCGGACTGGGGCTCAGAATGGAGCTGCTGGG NUP62 1727 TCATCTGCCACCACTGGACTCTCC 1728 AGCCTCTTTGCGTCAATAGCAACTGCTCCAACCTCATCTGCCA CCACTGGACTCTCCCTCTGTACCCCTGTGACCACAG OAZ1 1731 CTGCTCCTCAGCGAACTCCAGGAG 1732 AGCAAGGACAGCTTTGCAGTTCTCCTGGAGTTCGCTGAGGAG CAGCTGCGAGCCGACCATGTCTTC OCLN 1735 CTCCTCCCTCGGTGACCAATTCAC 1736 CCCTCCCATCCGAGTTTCAGGTGAATTGGTCACCGAGGGAGG AGGCCGACACACCACACCTACACTCCCGCGTC ODC1 1739 CCAGCGTTGGACAAATACTTTCCGTCA 1740 AGAGATCACCGGCGTAATCAACCCAGCGTTGGACAAATACTTT CCGTCAGACTCTGGAGTGAGAATCATAGCTGAGCCCG OLFML2B 1743 TGGCCTGGATCTCCTGAAGCTACA 1744 CATGTTGGAAGGAGCGTTCTATGGCCTGGATCTCCTGAAGCTA CATTCAGTCACCACCAAACTGGTG OLFML3 1747 CAGACGATCCACTCTCCCGGAGAT 1748 TCAGAACTGAGGCCGACACCATCTCCGGGAGAGTGGATCGTC TGGAGCGGGAGGTAGACTATCTGG OMD 1751 TCCGATGCACATTCAGCAACTCTACC 1752 CGCAAACTCAAGACTATCCCAAATATTCCGATGCACATTCAGC AACTCTACCTTCAGTTCAATGAAATTGAGGCTGTGACTG OR51E1 1755 TCCTCATCTCCACCTCATCCATGC 1756 GCATGCTTTCAGGCATTGACATCCTCATCTCCACCTCATCCAT GCCCAAAATGCTGGCCATCTTCT OR51E2 1759 ACATAGCCAGCACCCGTGTTCTGA 1760 TATGGTGCCAAAACCAAACAGATCAGAACACGGGTGCTGGCT ATGTTCAAGATCAGCTGTGACAAGGAC OSM 1763 CTGAGCTGGCCTCCTATGCCTCAT 1764 GTTTCTGAAGGGGAGGTCACAGCCTGAGCTGGCCTCCTATGC CTCATCATGTCCCAAACCAGACACCT PAGE1 1767 CCAACTCAAAGTCAGGATTCTACACCTGC 1768 CAACCTGACGAAGTGGAATCACCAACTCAAAGTCAGGATTCTA CACCTGCTGAAGAGAGAGAGGATGAGGGAGCATCTG PAGE4 1771 CCAACTGACAATCAGGATATTGAACCTGG 1772 GAATCTCAGCAAGAGGAACCACCAACTGACAATCAGGATATTG AACCTGGACAAGAGAGAGAAGGAACACCTCCGATCGAAGAAC PAK6 1775 AGTTTCAGGAAGGCTGCCCCTCTC 1776 CCTCCAGGTCACCCACAGCCAGTTTCAGGAAGGCTGCCCCTC TCTCCCACTAAGTTCTGGCCTGAAGGGAC PATE1 1779 CAGCACAGTTCTTTAGGCAGCCCA 1780 TGGTAATCCCTGGTTAACCTTCATGGGCTGCCTAAAGAACTGT GCTGATGTGAAAGGCATAAGGTGGA PCA3 1783 CTGAGATGCTCCCTGCCTTCAGTG 1784 CGTGATTGTCAGGAGCAAGACCTGAGATGCTCCCTGCCTTCAG TGTCCTCTGCATCTCCCCTTTCT PCDHGB7 1787 ATTCTTAAACAGCAAGCCCCGCC 1788 CCCAGCGTTGAAGCAGATAAGAAGATTCTTAAACAGCAAGCCC CGCCCAACACGGACTGGCGTTTC PCNA 1791 ATCCCAGCAGGCCTCGTTGATGAG 1792 GAAGGTGTTGGAGGCACTCAAGGACCTCATCAACGAGGCCTG CTGGGATATTAGCTCCAGCGGTGTAAACC PDE9A 1795 TACATCATCTGGGCCACGCAGAAG 1796 TTCCACAACTTCCGGCACTGCTTCTGCGTGGCCCAGATGATGT ACAGCATGGTCTGGCTCTGCAGTCT PDGFRB 1799 ATCAATGTCCCTGTCCGAGTGCTG 1800 CCAGCTCTCCTTCCAGCTACAGATCAATGTCCCTGTCCGAGTG CTGGAGCTAAGTGAGAGCCACCC PECAM1 1803 TTTATGAACCTGCCCTGCTCCCACA 1804 TGTATTTCAAGACCTCTGTGCACTTATTTATGAACCTGCCCTGC TCCCACAGAACACAGCAATTCCTCAGGCTAA PEX10 1807 CTACCTTCGGCACTACCGCTGAGC 1808 GGAGAAGTTCCCTCCCCAGAAGCTCATCTACCTTCGGCACTAC CGCTGAGCCGGCGCCCGGGTGGGCCTGGACACAGAT PGD 1811 ACTGCCCTCTCCTTCTATGACGGGT 1812 ATTCCCATGCCCTGTTTTACCACTGCCCTCTCCTTCTATGACGG GTACAGACATGAGATGCTTCCAGCCAG PGF 1815 ATCTTCTCAGACGTCCCGAGCCAG 1816 GTGGTTTTCCCTCGGAGCCCCCTGGCTCGGGACGTCTGAGAA GATGCCGGTCATGAGGCTGTTCCCTTGCT PGK1 1819 TCTCTGCTGGGCAAGGATGTTCTGTTC 1820 AGAGCCAGTTGCTGTAGAACTCAAATCTCTGCTGGGCAAGGAT GTTCTGTTCTTGAAGGACTGTGTAGGCCCAG PGR 1823 TAAATTGCCGTCGCAGCCGCA 1824 GATAAAGGAGCCGCGTGTCACTAAATTGCCGTCGCAGCCGCA GCCACTCAAGTGCCGGACTTGTGA PHTF2 1827 ACAATCTGGCAATGCACAGTTCCC 1828 GATATGGCTGATGCTGCTCCTGGGAACTGTGCATTGCCAGATT GTTTCCACAAGAACACCCAAACC PIK3C2A 1831 TGTGCTGTGACTGGACTTAACAAATAGC 1832 ATACCAATCACCGCACAAACCCAGGCTATTTGTTAAGTCCAGT CT CACAGCACAAAGAAACATATGCGGAGAAAATGCTAGTGTG PIK3CA 1835 TCCTGCTTCTCGGGATACAGACCA 1836 GTGATTGAAGAGCATGCCAATTGGTCTGTATCCCGAGAAGCAG GATTTAGCTATTCCCACGCAGGAC PIK3CG 1839 TTCTGGACAATTACTGCCACCCGA 1840 GGAGAACTCAATGTCCATCTCCATTCTTCTGGACAATTACTGC CACCCGATAGCCCTGCCTAAGCATCA PIM1 1843 TACACTCGGGTCCCATCGAAGTCC 1844 CTGCTCAAGGACACCGTCTACACGGACTTCGATGGGACCCGA GTGTATAGCCCTCCAGAGTGGATCC PLA2G7 1847 TGGCAATACATAAATCCTGTTGCCCA 1848 CCTGGCTGTGGTTTATCCTTTTGACTGGCAATACATAAATCCTG TTGCCCATATGAAATCATCAGCATGGGTCA PLAU 1851 AAGCCAGGCGTCTACACGAGAGTCTCAC 1852 GTGGATGTGCCCTGAAGGACAAGCCAGGCGTCTACACGAGAG TCTCACACTTCTTACCCTGGATCCGCAG PLAUR 1855 CATTGACTGCCGAGGCCCCATG 1856 CCCATGGATGCTCCTCTGAAGAGACTTTCCTCATTGACTGCCG AGGCCCCATGAATCAATGTCTGGTAGCCACCGG PLG 1859 TGCCAGGCCTGGGACTCTCA 1860 GGCAAAATTTCCAAGACCATGTCTGGACTGGAATGCCAGGCCT GGGACTCTCAGAGCCCACACGCTCATGGATACAT PLK1 1863 AACCCCGTGGCCGCCTCC 1864 AATGAATACAGTATTCCCAAGCACATCAACCCCGTGGCCGCCT CCCTCATCCAGAAGATGCTTCAGACA PLOD2 1867 TCCAGCCTTTTCGTGGTGACTCAA 1868 CAGGGAGGTGGTTGCAAATTTCTAAGGTACAATTGCTCTATTG AGTCACCACGAAAAGGCTGGAGCTTCATGCATCCTGGGAGA PLP2 1871 ACACCAGGCTACTCCTCCCTGTCG 1872 CCTGATCTGCTTCAGTGCCTCCACACCAGGCTACTCCTCCCTG TCGGTGATTGAGATGATCCTTGCTGC PNLIPRP2 1875 ACCCGTGCCTCCAGTCCACAC 1876 TGGAGAAGGTGAACTGCATCTGTGTGGACTGGAGGCACGGGT CCCGGGCAATGTACACCCAAGCCGTG POSTN 1879 TTCTCCATCTGGCCTCAGAGCAGA 1880 GTGGCCCAATTAGGCTTGGCATCTGCTCTGAGGCCAGATGGA GAATACACTTTGCTGGCACCTGTGA PPAP2B 1883 ACCAGGGCTCCTTGAGCAAATCCT 1884 ACAAGCACCATCCCAGTGATGTTCTGGCAGGATTTGCTCAAGG AGCCCTGGTGGCCTGCTGCATAGTTTTCTTCGTG PPFIA3 1887 CACCCACTTTACCTTCTGGTGCCC 1888 CCTGGAGCTCCGTTACTCTCAGGCACCCACTTTACCTTCTGGT GCCCACCTGGATCCCTATGTGGCT PPP1R12A 1891 CCGTTCTTCTTCCTTTCGAGCTGC 1892 CGGCAAGGGGTTGATATAGAAGCAGCTCGAAAGGAAGAAGAA CGGATCATGCTTAGAGATGCCAGGCA PPP3CA 1895 TACATGCGGTACCCTGCATCTTGG 1896 ATACTCCGAGCCCACGAAGCCCAAGATGCAGGGTACCGCATG TACAGGAAAAGCCAAACAACAGGCTTCC PRIMA1 1899 TGACGCATCCAGGGCTCTAGTCTG 1900 ATCCTCTTCCCTGAGCCGCTGACGCATCCAGGGCTCTAGTCTG CACATAAATTCCCTCTCAGCTGGG PRKAR1B 1903 AAGGCCATCTCCAAGAACGTGCTC 1904 ACAAAACCATGACTGCGCTGGCCAAGGCCATCTCCAAGAACG TGCTCTTCGCTCACCTGGATGACA PRKAR2B 1907 CGAACTGGCCTTAATGTACAATACACCCA 1908 TGATAATCGTGGGAGTTTCGGCGAACTGGCCTTAATGTACAAT ACACCCAGAGCAGCTACAATCACTGCTACCTCTCCTGGTGC PRKCA 1911 CAGCCTCTGCGGAATGGATCACACT 1912 CAAGCAATGCGTCATCAATGTCCCCAGCCTCTGCGGAATGGAT CACACTGAGAAGAGGGGGCGGATTTAC PRKCB 1915 CCAGACCATGGACCGCCTGTACTT 1916 GACCCAGCTCCACTCCTGCTTCCAGACCATGGACCGCCTGTA CTTTGTGATGGAGTACGTGAATGGG PROM1 1919 ACCCGAGGCTGTGTCTCCAACAC 1920 CTATGACAGGCATGCCACCCCGACCACCCGAGGCTGTGTCTC CAACACCGGAGGCGTCTTCCTCATGGTTGGAG PROS1 1923 CTCATCCTGACAGACTGCAGCTGC 1924 GCAGCACAGGAATCTTCTTCTTGGCAGCTGCAGTCTGTCAGGA TGAGATATCAGATTAGGTTGGATAGGTGGG PSCA 1927 CCTGTGAGTCATCCACGCAGTTCA 1928 ACCGTCATCAGCAAAGGCTGCAGCTTGAACTGCGTGGATGAC TCACAGGACTACTACGTGGGCAAGAAGAACATCACG PSMD13 1931 CCTGAAGTGTCAGCTGATGCCACA 1932 GGAGGAGCTCTACACGAAGAAGTTGTGGCATCAGCTGACACT TCAGGTGCTTGATTTTGTGCAGGATCCG PTCH1 1935 CCTGAAACAAGGCTGAGAATCCCG 1936 CCACGACAAAGCCGACTACATGCCTGAAACAAGGCTGAGAAT CCCGGCAGCAGAGCCCATCGAGTA PTEN 1939 CCTTTCCAGCTTTACAGTGAATTGCTGCA 1940 TGGCTAAGTGAAGATGACAATCATGTTGCAGCAATTCACTGTA AAGCTGGAAAGGGACGAACTGGTGTAATGATATGTGCA PTGER3 1943 CCTTTGCCTTCCTGGGGCTCTT 1944 TAACTGGGGCAACCTTTTCTTCGCCTCTGCCTTTGCCTTCCTG GGGCTCTTGGCGCTGACAGTCACCTTTTCCTGCAA PTGS2 1947 CCTACCACCAGCAACCCTGCCA 1948 GAATCATTCACCAGGCAAATTGCTGGCAGGGTTGCTGGTGGTA GGAATGTTCCACCCGCAGTACAG PTH1R 1951 CCAGTGCCAGTGTCCAGCGGCT 1952 CGAGGTACAAGCTGAGATCAAGAAATCTTGGAGCCGCTGGAC ACTGGCACTGGACTTCAAGCGAAAGGCACGC PTHLH 1955 TGACACCTCCACAACGTCGCTGGA 1956 AGTGACTGGGAGTGGGCTAGAAGGGGACCACCTGTCTGACAC CTCCACAACGTCGCTGGAGCTCGATTCACGGTAACAGGCTT PTK2 1959 ACCAGGCCCGTCACATTCTCGTAC 1960 GACCGGTCGAATGATAAGGTGTACGAGAATGTGACGGGCCTG GTGAAAGCTGTCATCGAGATGTCCAG PTK2B 1963 CTCCGCAAACCAACCTCCTGGCT 1964 CAAGCCCAGCCGACCTAAGTACAGACCCCCTCCGCAAACCAA CCTCCTGGCTCCAAAGCTGCAGTTCCAGGTTC PTK6 1967 AGTGTCTGCGTCCAATACACGCGT 1968 GTGCAGGAAAGGTTCACAAATGTGGAGTGTCTGCGTCCAATAC ACGCGTGTGCTCCTCTCCTTACTCCATCGTGTGTGC PTK7 1971 CGCAAGGTCCCATTCTTGAAGACC 1972 TCAGAGGACTCACGGTTCGAGGTCTTCAAGAATGGGACCTTGC GCATCAACAGCGTGGAGGTGTATG PTPN1 1975 CTGATCCAGACAGCCGACCAGCT 1976 AATGAGGAAGTTTCGGATGGGGCTGATCCAGACAGCCGACCA GCTGCGCTTCTCCTACCTGGCTGTGATCGAAG PTPRK 1979 CCCCATCGTTGTACATTGCAGTGC 1980 TCAAACCCTCCCAGTGCTGGCCCCATCGTTGTACATTGCAGTG CTGGTGCTGGACGAACTGGCTGCT PTTG1 1983 CACACGGGTGCCTGGTTCTCCA 1984 GGCTACTCTGATCTATGTTGATAAGGAAAATGGAGAACCAGGC ACCCGTGTGGTTGCTAAGGATGGGCTGAAGC PYCARD 1987 ACGTTTGTGACCCTCGCGATAAGC 1988 CTTTATAGACCAGCACCGGGCTGCGCTTATCGCGAGGGTCAC AAACGTTGAGTGGCTGCTGGATGCT RAB27A 1991 ACAAATTGCTTCTCACCATCCCCATT 1992 TGAGAGATTAATGGGCATTGTGTACAAATTGCTTCTCACCATCC CCATTAGACCTACGAATAAAGCATCCGG RAB30 1995 CCATCAGGGCAGTTGCTGATTCCT 1996 TAAAGGCTGAGGCACGGAGAAGAAAAGGAATCAGCAACTGCC CTGATGGGCCATGAGATGCTGGGGAG RAB31 1999 CTTCTCAAAGTGAGGTGCCAGGCC 2000 CTGAAGGACCCTACGCTCGGTGGCCTGGCACCTCACTTTGAG AAGAGTGAGCACACTGGCTTTGCAT RAD21 2003 CACTTAAAACGAATCTCAAGAGGGTGAC 2004 TAGGGATGGTATCTGAAACAACAATGGTCACCCTCTTGAGATT CA CGTTTTAAGTGTAATTCCATAATGAGCAGAGGTGTACGCGA RAD51 2007 CTTTCAGCCAGGCAGATGCACTTG 2008 AGACTACTCGGGTCGAGGTGAGCTTTCAGCCAGGCAGATGCA CTTGGCCAGGTTTCTGCGGATGCT RAD9A 2011 CTTTGCTGGACGGCCACTTTGTCT 2012 GCCATCTTCACCATCAAGGACTCTTTGCTGGACGGCCACTTTG TCTTGGCCACACTCTCAGACACCG RAF1 2015 TCCAGGATGCCTGTTAGTTCTCAGCA 2016 CGTCGTATGCGAGAGTCTGTTTCCAGGATGCCTGTTAGTTCTC AGCACAGATATTCTACACCTCACGCCTTCA RAGE 2019 CCGGAGTGTCTATTCCAAGCAGCC 2020 ATTAGGGGACTTTGGCTCCTGCCGGAGTGTCTATTCCAAGCAG CCGTACACGGAATACATCTCCACCC RALA 2023 TTGTGTTTCTTGGGCAGTCTTTCTTGAA 2024 TGGTCCTGAATGTAGCGTGTAAGCTTGTGTTTCTTGGGCAGTC TTTCTTGAAATTGAAGAGGTGAAATGGGG RALBP1 2027 TGCTGTCCTGTCGGTCTCAGTACGTTCA 2028 GGTGTCAGATATAAATGTGCAAATGCCTTCTTGCTGTCCTGTC GGTCTCAGTACGTTCACTTTATAGCTGCTGGCAATATCGAA RAP1B 2031 CACGCATGATGCAAGCTTGTCAAA 2032 TGACAGCGTGAGAGGTACTAGGTTTTGACAAGCTTGCATCATG CGTGAGTATAAGCTAGTCGTTCTTGGCTCAG RARB 2035 TGTGCTCTGCTGTGTTCCCACTTG 2036 ATGAACCCTTGACCCCAAGTTCAAGTGGGAACACAGCAGAGC ACAGTCCTAGCATCTCACCCAGCTC RASSF1 2039 CACCACCAAGAACTTTCGCAGCAG 2040 AGGGCACGTGAAGTCATTGAGGCCCTGCTGCGAAAGTTCTTG GTGGTGGATGACCCCCGCAAGTTTGCACTCTTT RB1 2043 CCCTTACGGATTCCTGGAGGGAAC 2044 CGAAGCCCTTACAAGTTTCCTAGTTCACCCTTACGGATTCCTG GAGGGAACATCTATATTTCACCCCTGAAGAGTCC RECK 2047 TCAAGTGTCCTTCGCTCTTGGCAG 2048 GTCGCCGAGTGTGCTTCTGTCAAGTGTCCTTCGCTCTTGGCAG CTGGATGCAAACCCATCATCCCAC REG4 2051 TCCTCTTCCTTTCTGCTAGCCTGGC 2052 TGCTAACTCCTGCACAGCCCCGTCCTCTTCCTTTCTGCTAGCC TGGCTAAATCTGCTCATTATTTCAGAGGGGAAACCTAGCA RELA 2055 CTGAGCTCTGCCCGGACCGCT 2056 CTGCCGGGATGGCTTCTATGAGGCTGAGCTCTGCCCGGACCG CTGCATCCACAGTTTCCAGAACCTGG RFX1 2059 TCCAATGGACCAAGCACTGTGACA 2060 TCCTCTCCAAGTTCGAGCCCGTGCTCCAATGGACCAAGCACTG TGACAACGTGCTGTACCAGGGCCTG RGS10 2063 AGTTCCAGCAGCAGCCACCAGAG 2064 AGACATCCACGACAGCGATGGCAGTTCCAGCAGCAGCCACCA GAGCCTCAAGAGCACAGCCAAATGG RGS7 2067 TGAAAATGAACTCCCACTTCCGGG 2068 CAGGCTGCAGAGAGCATTTGCCCGGAAGTGGGAGTTCATTTTC ATGCAAGCAGAAGCACAAGCAAA RHOA 2071 AAATGGGCTCAACCAGAAAAGCCC 2072 TGGCATAGCTCTGGGGTGGGCAGTTTTTTGAAAATGGGCTCAA CCAGAAAAGCCCAAGTTCATGCAGCTGTGGCA RHOB 2075 CTTTCCAACCCCTGGGGAAGACAT 2076 AAGCATGAACAGGACTTGACCATCTTTCCAACCCCTGGGGAAG ACATTTGCAACTGACTTGGGGAGG RHOC 2079 TCCGGTTCGCCATGTCCCG 2080 CCCGTTCGGTCTGAGGAAGGCCGGGACATGGCGAACCGGATC AGTGCCTTTGGCTACCTTGAGTGCTC RLN1 2083 TGAGAGGCAACCATCATTACCAGAGC 2084 AGCTGAAGGCAGCCCTATCTGAGAGGCAACCATCATTACCAG AGCTACAGCAGTATGTACCTGCATTAAAGGATTCCAA RND3 2087 TTTTAAGCCTGACTCCTCACCGCG 2088 TCGGAATTGGACTTGGGAGGCGCGGTGAGGAGTCAGGCTTAA AACTTGTTGGAGGGGAGTAACCAG RNF114 2091 CCAGGTCAGCCCTTCTCTTCCCTT 2092 TGACAGGGGAAGTGGGTCCCCAGGTCAGCCCTTCTCTTCCCT TTGGGCTCTTGCCAAAGCTGTCTTCC ROBO2 2095 CTGTACCATCCACTGCCAGCGTTT 2096 CTACAAGGCCCAGCCAACCAAACGCTGGCAGTGGATGGTACA GCGTTACTGAAATGTAAAGCCACTGGTG RRM1 2099 CATTGGAATTGCCATTAGTCCCAGC 2100 GGGCTACTGGCAGCTACATTGCTGGGACTAATGGCAATTCCAA TGGCCTTGTACCGATGCTGAGAG RRM2 2103 CCAGCACAGCCAGTTAAAAGATGCA 2104 CAGCGGGATTAAACAGTCCTTTAACCAGCACAGCCAGTTAAAA GATGCAGCCTCACTGCTTCAACGCAGAT S100P 2107 TTGCTCAAGGACCTGGACGCCAA 2108 AGACAAGGATGCCGTGGATAAATTGCTCAAGGACCTGGACGC CAATGGAGATGCCCAGGTGGACTTC SAT1 2111 TCCAGTGCTCTTTCGGCACTTCTG 2112 CCTTTTACCACTGCCTGGTTGCAGAAGTGCCGAAAGAGCACTG GACTCCGGAAGGACACAGCATTGT SCUBE2 2115 CAGGCCCTCTTCCGAGCGGT 2116 TGACAATCAGCACACCTGCATTCACCGCTCGGAAGAGGGCCT GAGCTGCATGAATAAGGATCACGGCTGTAGTCACA SDC1 2119 CTCTGAGCGCCTCCATCCAAGG 2120 GAAATTGACGAGGGGTGTCTTGGGCAGAGCTGGCTCTGAGCG CCTCCATCCAAGGCCAGGTTCTCCGTTAGCTCCT SDC2 2123 AACTCCATCTCCTTCCCCAGGCAT 2124 GGATTGAAGTGGCTGGAAAGAGTGATGCCTGGGGAAGGAGAT GGAGTTATGAGGGTACTGTGGCTGGT SDHC 2127 TTACATCCTCCCTCTCCCCGCAAT 2128 CTTCCCTCGGGTCTCAGGCATTTACATCCTCCCTCTCCCCGCA ATCTGACCTTTACCAGGAGGGAA SEC14L1 2131 CGGGCTTCTACATCCTGCAGTGG 2132 AGGGTTCCCATGTGACCAGGTGGCCGGGCTTCTACATCCTGC AGTGGAAATTCCACAGCATGCCTGC SEC23A 2135 TCCTGGAGATGAAATGCTGTCCCA 2136 CGTGTGCATTAGATCAGACAGGTCTCCTGGAGATGAAATGCTG TCCCAACCTTACTGGAGGATACATGGTAATGGG SEMA3A 2139 TTGCCAATAGACCAGCGCTCTCTG 2140 TTGGAATGCAGTCCGAAGTCGCAGAGAGCGCTGGTCTATTGG CAATTCCAGAGGCGAAATGAAGAG SEPT9 2143 TTGCCAATAGACCAGCGCTCTCTG 2144 CAGTGACCACGAGTACCAGGTCAACGGCAAGAGGATCCTTGG GAGGAAGACCAAGTGGGGTACCATCGAAG SERPINA3 2147 AGGGAATCGCTGTCACCTTCCAAG 2148 GTGTGGCCCTGTCTGCTTATCCTTGGAAGGTGACAGCGATTCC CTGTGTAGCTCTCACATGCACAGGG SERPINB5 2151 AGCTGACAACAGTGTGAACGACCAGACC 2152 CAGATGGCCACTTTGAGAACATTTTAGCTGACAACAGTGTGAA CGACCAGACCAAAATCCTTGTGGTTAATGCTGCC SESN3 2155 TGCTCTTCTCCTCGTCTGGCAAAG 2156 GACCCTGGTTTTGGGTATGAAGACTTTGCCAGACGAGGAGAA GAGCATTTGCCAACATTCCGAGCTC SFRP4 2159 CCTGGGACAGCCTATGTAAGGCCA 2160 TACAGGATGAGGCTGGGCATTGCCTGGGACAGCCTATGTAAG GCCATGTGCCCCTTGCCCTAACAAC SH3RF2 2163 AACCGGATGGTCCATTCTCCTTCA 2164 CCATCACAACAGCCTTGAACACTCTCAACCGGATGGTCCATTC TCCTTCAGGGCGCCATATGGTAGAGATCAGCACCCCAGTG SH3YL1 2167 CACAGCAGTCATCTGCACCAGTCC 2168 CCTCCAAAGCCATTGTCAAGACCACAGCAGTCATCTGCACCAG TCCAGCTGAACTCTGGCTCTCAAAG SHH 2171 CACCGAGTTCTCTGCTTTCACCGA 2172 GTCCAAGGCACATATCCACTGCTCGGTGAAAGCAGAGAACTC GGTGGCGGCCAAATCGGGAGGCTGCTTC SHMT2 2175 CCATCACTGCCAACAAGAACACCTG 2176 AGCGGGTGCTAGAGCTTGTATCCATCACTGCCAACAAGAACAC CTGTCCTGGAGACCGAAGTGCCAT SIM2 2179 CGCCTCTCCACGCACTCAGCTAT 2180 GATGGTAGGAAGGGATGTGCCCGCCTCTCCACGCACTCAGCT ATACCTCATTCACAGCTCCTTGTG SIPA1L1 2183 CGCCACAATGCCCTCATAGTTGAC 2184 CTAGGACAGCTTGGCTTCCATGTCAACTATGAGGGCATTGTGG CGGATGTGGAGCCCTACGGTTATG SKIL 2187 CCAATCTCTGCCTCAGTTCTGCCA 2188 AGAGGCTGAATATGCAGGACAGTTGGCAGAACTGAGGCAGAG ATTGGACCATGCTGAGGCCGATAG SLC22A3 2191 CAGCATCCACGCATTGACACAGAC 2192 ATCGTCAGCGAGTTTGACCTTGTCTGTGTCAATGCGTGGATGC TGGACCTCACCCAAGCCATCCTG SLC25A21 2195 TCATGGTGCTGCATAGCAAATATCCA 2196 AAGTGTTTTTCCCCCTTGAGATAATGGATATTTGCTATGCAGCA CCATGAAGAAGAGAGACTATCGATCGGCC SLC44A1 2199 TACCATGGCTGCTGCTCTTCATCC 2200 AGGACCGTAGCTGCACAGACATACCATGGCTGCTGCTCTTCAT CCTCTTCTGCATTGGGATGGGAT SMAD4 2203 TGCATTCCAGCCTCCCATTTCCA 2204 GGACATTACTGGCCTGTTCACAATGAGCTTGCATTCCAGCCTC CCATTTCCAATCATCCTGCTCCTGAGTATTGGT SMARCC2 2207 TATCTTACCTCTACCGCCTGCCGC 2208 TACCGACTGAACCCCCAAGAGTATCTTACCTCTACCGCCTGCC GCCGAAACCTAGCGGGTGATGTC SMARCD1 2211 CCCACCCTTGCTGTGTTGAGTCTG 2212 CCGAGTTAGCATATCCCAGGCTCGCAGACTCAACACAGCAAG GGTGGGAGACAGCTGGGCACAAAGG SMO 2215 CTTCACAGAGGCTGAGCACCAGGA 2216 GGCATCCAGTGCCAGAACCCGCTCTTCACAGAGGCTGAGCAC CAGGACATGCACAGCTACATCGCG SNAI1 2219 TCTGGATTAGAGTCCTGCAGCTCGC 2220 CCCAATCGGAAGCCTAACTACAGCGAGCTGCAGGACTCTAAT CCAGAGTTTACCTTCCAGCAGCCCTAC SNRPB2 2223 CCCACCTAAGGCCTACGCCGACTA 2224 CGTTTCCTGCTTTTGGTTCTTACAGTAGTCGGCGTAGGCCTTA GGTGGGTTCGTGCGCCTTCTACCT SOD1 2227 TTTGTCAGCAGTCACATTGCCCAA 2228 TGAAGAGAGGCATGTTGGAGACTTGGGCAATGTGACTGCTGA CAAAGATGGTGTGGCCGATGTGTCTATT SORBS1 2231 ATTTCCATTGGCATCAGCACTGGA 2232 GCAGATGAGTGGAGGCTTTCTTCCAGTGCTGATGCCAATGGAA ATGCCCAGCCCTCTTCACTCGCT SOX4 2235 CGAGTCCAGCATCTCCAACCTGGT 2236 AGATGATCTCGGGAGACTGGCTCGAGTCCAGCATCTCCAACC TGGTTTTCACCTACTGAAGGGCGC SPARC 2239 TGGACCAGCACCCCATTGACGG 2240 TCTTCCCTGTACACTGGCAGTTCGGCCAGCTGGACCAGCACC CCATTGACGGGTACCTCTCCCACACCGAGCT SPARCL1 2243 ACTTCATCCCAAGCCAGGCCTTTC 2244 GGCACAGTGCAAGTGATGACTACTTCATCCCAAGCCAGGCCTT TCTGGAGGCCGAGAGAGCTCAATC SPDEF 2247 ATCATCCGGAAGCCAGACATCTCC 2248 CCATCCGCCAGTATTACAAGAAGGGCATCATCCGGAAGCCAG ACATCTCCCAGCGCCTCGTCTACCAGTTCGTGCACCC SPINK1 2251 ACCACGTCTCTTCAGAAGCCTGGG 2252 CTGCCATATGACCCTTCCAGTCCCAGGCTTCTGAAGAGACGTG GTAAGTGCGGTGCAGTTTTCAAC SPINT1 2255 CTGTCGCAGTGTTCCTGGTCATCTGC 2256 ATTCCCAGCACAGGCTCTGTGGAGATGGCTGTCGCAGTGTTC CTGGTCATCTGCATTGTGGTGGTGGTAGCCATCT SPP1 2259 TGAATGGTGCATACAAGGCCATCC 2260 TCACACATGGAAAGCGAGGAGTTGAATGGTGCATACAAGGCC ATCCCCGTTGCCCAGGACCTGAAC SQLE 2263 TGGGCAAGAAAAACATCTCATTCCTTTG 2264 ATTTTCGAGGCCAAAAAATCATTTTACTGGGCAAGAAAAACATC TCATTCCTTTGTCGTGAATATCCTTGCTCAGG SRC 2267 AACCGCTCTGACTCCCGTCTGGTG 2268 TGAGGAGTGGTATTTTGGCAAGATCACCAGACGGGAGTCAGA GCGGTTACTGCTCAATGCAGAGAACCCGAGAG SRD5A1 2271 CCTCTCTCGGAGGCCACAGAGGCT 2272 GGGCTGGAATCTGTCTAGGAGCCCTCTCTCGGAGGCCACAGA GGCTGGGGGTAGCCATTGTGCAGTCATGG SRD5A2 2275 AGACACCACTCAGAATCCCCAGGC 2276 GTAGGTCTCCTGGCGTTCTGCCAGCTGGCCTGGGGATTCTGA GTGGTGTCTGCTTAGAGTTTACTCCTACCCTTCCAGGGA STS 2279 AGTCACGAGCACCCAGCGAAACTT 2280 CCTGTCCTGCCAGAGCATGGATGAAGTTTCGCTGGGTGCTCGT GACTGGCCAGTTTTGTGCAGCTG STAT1 2283 TGGCAGTTTTCTTCTGTCACCAAAA 2284 GGGCTCAGCTTTCAGAAGTGCTGAGTTGGCAGTTTTCTTCTGT CACCAAAAGAGGTCTCAATGTGGACCAGCTGAACATGT STAT3 2287 TCCTGGGAGAGATTGACCAGCA 2288 TCACATGCCACTTTGGTGTTTCATAATCTCCTGGGAGAGATTGA CCAGCAGTATAGCCGCTTCCTGCAAG STAT5A 2291 CGGTTGCTCTGCACTTCGGCCT 2292 GAGGCGCTCAACATGAAATTCAAGGCCGAAGTGCAGAGCAAC CGGGGCCTGACCAAGGAGAACCTCGTGTTCCTGGC STAT5B 2295 CAGCCAGGACAACAATGCGACGG 2296 CCAGTGGTGGTGATCGTTCATGGCAGCCAGGACAACAATGCG ACGGCCACTGTTCTCTGGGACAATGCTTTTGC STMN1 2299 CACGTTCTCTGCCCCGTTTCTTG 2300 AATACCCAACGCACAAATGACCGCACGTTCTCTGCCCCGTTTC TTGCCCCAGTGTGGTTTGCATTGTCTCC STS 2303 CTGCGTGGCTCTCGGCTTCCCA 2304 GAAGATCCCTTTCCTCCTACTGTTCTTTCTGTGGGAAGCCGAG AGCCACGCAGCATCAAGGCCGAACATCATCC SULF1 2307 TACCGTGCCAGCAGAAGCCAAAG 2308 TGCAGTTGTAGGGAGTCTGGTTACCGTGCCAGCAGAAGCCAA AGAAAGAGTCAACGGCAATTCTTGAGA SUMO1 2311 CTGACCAGGAGGCAAAACCTTCAACTGA 2312 GTGAAGCCACCGTCATCATGTCTGACCAGGAGGCAAAACCTTC AACTGAGGACTTGGGGGATAAGAAGGAAGG SVIL 2315 ACCCCAGGACTGATGTCAAGGCAT 2316 ACTTGCCCAGCACAAGGAAGACCCCAGGACTGATGTCAAGGC ATACGATGTGACACGGATGGTGTC TAF2 2319 AGCCTCCAAACACAGTGACCACCA 2320 GCGCTCCACTCTCAGTCTTTACTAAGGAATCTACAGCCTCCAA ACACAGTGACCACCATCACCACCATCACCATGAGCACAAG TARP 2323 TCTTCATGGTGTTCCCCTCCTGG 2324 GAGCAACACGATTCTGGGATCCCAGGAGGGGAACACCATGAA GACTAACGACACATACATGAAATTTAGCTGGTTAACGGTGCC TBP 2327 TACCGCAGCAAACCGCTTGGG 2328 GCCCGAAACGCCGAATATAATCCCAAGCGGTTTGCTGCGGTA ATCATGAGGATAAGAGAGCCACG TFDP1 2331 CGCACCAGCATGGCAATAAGCTTT 2332 TGCGAAGTGCTTTTGTTTGTTTGTTTTCGTTTGGTTAAAGCTTAT TGCCATGCTGGTGCGGCTATGGAGACTGTCTGGAAGGC TFF1 2335 TGCTGTTTCGACGACACCGTTCG 2336 GCCCTCCCAGTGTGCAAATAAGGGCTGCTGTTTCGACGACAC CGTTCGTGGGGTCCCCTGGTGCTTCTATCCTAATACCATCGAC G TFF3 2339 CAGAAGCGCTTGCCGGGAGCAAAGG 2340 AGGCACTGTTCATCTCAGCTTTTCTGTCCCTTTGCTCCCGGCA AGCGCTTCTGCTGAAAGTTCATATCTGGAGCCTGATG TGFA 2343 TTGGCCTGTAATCACCTGTGCAGCCTT 2344 GGTGTGCCACAGACCTTCCTACTTGGCCTGTAATCACCTGTGC AGCCTTTTGTGGGCCTTCAAAACTCTGTCAAGAACTCCGT TGFB1I1 2347 CAAGATGTGGCTTCTGCAACCAGC 2348 GCTACTTTGAGCGCTTCTCGCCAAGATGTGGCTTCTGCAACCA GCCCATCCGACACAAGATGGTGACC TGFB2 2351 TCCTGAGCCCGAGGAAGTCCC 2352 ACCAGTCCCCCAGAAGACTATCCTGAGCCCGAGGAAGTCCCC CCGGAGGTGATTTCCATCTACAACAGCACCAGG TGFB3 2355 CGGCCAGATGAGCACATTGCC 2356 GGATCGAGCTCTTCCAGATCCTTCGGCCAGATGAGCACATTGC CAAACAGCGCTATATCGGTGGC TGFBR2 2359 TTCTGGGCTCCTGATTGCTCAAGC 2360 AACACCAATGGGTTCCATCTTTCTGGGCTCCTGATTGCTCAAG CACAGTTTGGCCTGATGAAGAGG THBS2 2363 TGAGTCTGCCATGACCTGTTTTCCTTCAT 2364 CAAGACTGGCTACATCAGAGTCTTAGTGCATGAAGGAAAACAG GTCATGGCAGACTCAGGACCTATCTATGACCAAACCTACGCTG THY1 2367 CAAGCTCCCAAGAGCTTCCAGAGC 2368 GGACAAGACCCTCTCAGGCTGTCCCAAGCTCCCAAGAGCTTC CAGAGCTCTGACCCACAGCCTCCAA TIAM1 2371 TGGAGCCCTTCTCCCAAGATGGTA 2372 GTCCCTGGCTGAAAATGGCCTGGAGCCCTTCTCCCAAGATGG TACCCTAGAAGACTTCGGGAGCCC TIMP2 2375 CCCTGGGACACCCTGAGCACCA 2376 TCACCCTCTGTGACTTCATCGTGCCCTGGGACACCCTGAGCAC CACCCAGAAGAAGAGCCTGAACCACA TIMP3 2379 CCAAGAACGAGTGTCTCTGGACCG 2380 CTACCTGCCTTGCTTTGTGACTTCCAAGAACGAGTGTCTCTGG ACCGACATGCTCTCCAATTTCGGT TK1 2383 CAAATGGCTTCCTCTGGAAGGTCCCA 2384 GCCGGGAAGACCGTAATTGTGGCTGCACTGGATGGGACCTTC CAGAGGAAGCCATTTGGGGCCATCCTGAACCTGGTGCCGCTG TMPRSS2 2387 AAGCACTGTGCATCACCTTGACCC 2388 GGACAGTGTGCACCTCAAAGACTAAGAAAGCACTGTGCATCAC CTTGACCCTGGGGACCTTCCTCGTGGGAG TMPRSS2 2391 TAAGGCTTCCTGCCGCGCTCCA 2392 GAGGCGGAGGCGGAGGGCGAGGGGCGGGGAGCGCCGCCTG ERGA GAGCGCGGCAGGAAGCCTTATCAGTTGTGAGTGAGGACCAGT TMPRSS2 2395 CCTGGAATAACCTGCCGCGC 2396 GAGGCGGAGGGCGAGGGGCGGGGAGCGCCGCCTGGAGCGC ERGB GGCAGGTTATTCCAGGATCTTTGGAGACCCGAGGAA TNF 2399 CGCTGAGATCAATCGGCCCGACTA 2400 GGAGAAGGGTGACCGACTCAGCGCTGAGATCAATCGGCCCGA CTATCTCGACTTTGCCGAGTCTGGGCA TNFRSF10A 2403 CAATGCTTCCAACAATTTGTTTGCTTGCC 2404 TGCACAGAGGGTGTGGGTTACACCAATGCTTCCAACAATTTGT TTGCTTGCCTCCCATGTACAGCTTGTAAATCAGATGAAGA TNFRSF10B 2407 CAGACTTGGTGCCCTTTGACTCC 2408 CTCTGAGACAGTGCTTCGATGACTTTGCAGACTTGGTGCCCTT TGACTCCTGGGAGCCGCTCATGAGGAAGTTGGGCCTCATGG TNFRSF18 2411 CCTTCTCCTCTGCCGATCGCTC 2412 CAGAAGCTGCCAGTTCCCCGAGGAAGAGCGGGGCGAGCGAT CGGCAGAGGAGAAGGGGCGGCTGGGAGACCTGTGGGTG TNFSF10 2415 AAGTACACGTAAGTTACAGCCACACA 2416 CTTCACAGTGCTCCTGCAGTCTCTCTGTGTGGCTGTAACTTAC GTGTACTTTACCAACGAGCTGAAGCAGATG TNFSF11 2419 ACATGACCAGGGACCAACCCCTC 2420 AACTGCATGTGGGCTATGGGAGGGGTTGGTCCCTGGTCATGT GCCCCTTCGCAGCTGAAGTGGAGAGGGTGTCA TOP2A 2423 CATATGGACTTTGACTCAGCTGTGGC 2424 AATCCAAGGGGGAGAGTGATGACTTCCATATGGACTTTGACTC AGCTGTGGCTCCTCGGGCAAAATCTGTAC TP53 2427 AAGTCCTGGGTGCTTCTGACGCACA 2428 CTTTGAACCCTTGCTTGCAATAGGTGTGCGTCAGAAGCACCCA GGACTTCCATTTGCTTTGTCCCGGG TP63 2431 CCCGGGTCTCACTGGAGCCCA 2432 CCCCAAGCAGTGCCTCTACAGTCAGTGTGGGCTCCAGTGAGA CCCGGGGTGAGCGTGTTATTGATGCTGTGCGATTC TPD52 2435 TCTGCTACCCACTGCCAGATGCTG 2436 GCCTGTGAGATTCCTACCTTTGTTCTGCTACCCACTGCCAGAT GCTGCAAGCGAGGTCCAAGCACAT TPM1 2439 TTCTCCAGCTGACCCTGGTTCTCTC 2440 TCTCTGAGCTCTGCATTTGTCTATTCTCCAGCTGACCCTGGTTC TCTCTCTTAGCATCCTGCCTTAGAGCC TPM2 2443 CCAAGCACATCGCTGAGGATTCAG 2444 AGGAGATGCAGCTGAAGGAGGCCAAGCACATCGCTGAGGATT CAGACCGCAAATATGAAGAGGTGG TPP2 2447 ATCCTGTTCAGGTGGCTGCACCTT 2448 TAACCGTGGCATCTACCTCCGAGATCCTGTTCAGGTGGCTGCA CCTTCAGATCATGGCGTTGGCAT TPX2 2451 CAGGTCCCATTGCCGGGCG 2452 TCAGCTGTGAGCTGCGGATACCGCCCGGCAATGGGACCTGCT CTTAACCTCAAACCTAGGACCGT TRA2A 2455 AACTGAGGCCAAACACTCCAAGGC 2456 GCAAATCCAGATCCCAACACTTGCCTTGGAGTGTTTGGCCTCA GTTTGTACACAACAGAGAGGGATCTTCGTGAAG TRAF3IP2 2459 TGGATCTGCCAACCATAGACACGG 2460 CCTCACAGGAACCGAGCAGGCCTGGATCTGCCAACCATAGAC ACGGGATATGATTCCCAGCCCCAG TRAM1 2463 AGTGCTGAGCCACGAATTCGTCC 2464 CAAGAAAAGCACCAAGAGCCCCCCAGTGCTGAGCCACGAATT CGTCCTGCAGAATCACGCGGACAT TRAP1 2467 TTCGGCGATTTCAAACACTCCAGA 2468 TTACCAGTGGCTTTCAGATGGTTCTGGAGTGTTTGAAATCGCC GAAGCTTCGGGAGTTAGAACCGGGACA TRIM14 2471 AACTGCCAGCTCTCAGACCCTTCC 2472 CATTCGCCTTAAGGAAAGCATAAACTGCCAGCTCTCAGACCCT TCCAGCACCAAGCCAGGTACCTTG TRO 2475 CCACCCAAGGCCAAATTACCAATG 2476 GCAACTGCCACCCATACAGCTACCACCCAAGGCCAAATTACCA ATGAGACAGCCAGTATCCACACCA TRPC6 2479 CTTCTCCCAGCTCCGAGTCCATG 2480 CGAGAGCCAGGACTATCTGCTCATGGACTCGGAGCTGGGAGA AGACGGCTGCCCGCAAGCCCCGCTGCCTTGCTACGGCTA TRPV6 2483 ACTTTGGGGAGCACCCTTTGTCCT 2484 CCGTAGTCCCTGCAACCTCATCTACTTTGGGGAGCACCCTTTG TCCTTTGCTGCCTGTGTGAACAGTGAGGA TSTA3 2487 AACGTGCACATGAACGACAACGTC 2488 CAATTTGGACTTCTGGAGGAAAAACGTGCACATGAACGACAAC GTCCTGCACTCGGCCTTTGAGGTG TUBB2A 2491 TCTCAGATCAATCGTGCATCCTTAGTGAA 2492 CGAGGACGAGGCTTAAAAACTTCTCAGATCAATCGTGCATCCT TAGTGAACTTCTGTTGTCCTCAAGCATGGT TYMP 2495 ACAGCCTGCCACTCATCACAGCC 2496 CTATATGCAGCCAGAGATGTGACAGCCACCGTGGACAGCCTG CCACTCATCACAGCCTCCATTCTCAGTAAGAAACTCGTGG TYMS 2499 CATCGCCAGCTACGCCCTGCTC 2500 GCCTCGGTGTGCCTTTCAACATCGCCAGCTACGCCCTGCTCAC GTACATGATTGCGCACATCACG UAP1 2503 TACCTGTAAACCTTTCTCGGCGCG 2504 CTGGAGACGGTCGTAGCTGCGGTCGCGCCGAGAAAGGTTTAC AGGTACATACATTACACCCCTATTTCTACAAAGCTTGGC UBE2C 2507 TCTGCCTTCCCTGAATCAGACAACC 2508 TGTCTGGCGATAAAGGGATTTCTGCCTTCCCTGAATCAGACAA CCTTTTCAAATGGGTAGGGACCAT UBE2G1 2511 TTGTCCCACCAGTGCCTCATCAGT 2512 TGACACTGAACGAGGTGGCTTTTGTCCCACCAGTGCCTCATCA GTGTGAGGCGATTCCTCTCTGCTT UBE2T 2515 AGGTGCTTGGAGACCATCCCTCAA 2516 TGTTCTCAAATTGCCACCAAAAGGTGCTTGGAGACCATCCCTC AACATCGCAACTGTGTTGACCTCT UGDH 2519 TATACAGCACACAGGGCCTGCACA 2520 GAAACTCCAGAGGGCCAGAGAGCTGTGCAGGCCCTGTGTGCT GTATATGAGCACTGGGTTCCCAGAG UGT2B15 2523 AAAGATGGGACTCCTCCTTTATTTCAGCA 2524 AAGCCTGAAGTGGAATGACTGAAAGATGGGACTCCTCCTTTAT TTCAGCATGGAGGGTTTTAAATGGAGG UGT2B17 2527 ACCCGAAGGTGCTTGGCTCCTTTA 2528 TTGAGTTTGTCATGCGCCATAAAGGAGCCAAGCACCTTCGGGT CGCAGCCCACAACCTCACCTGGA UHRF1 2531 CGGCCATACCCTCTTCGACTACGA 2532 CTACAGGGGCAAACAGATGGAGGACGGCCATACCCTCTTCGA CTACGAGGTCCGCCTGAATGACACC UTP23 2535 TCGAAATTGTCCTCATTTCAAGAATGCA 2536 GATTGCACAAAAATGCCAAGTTCGAAATTGTCCTCATTTCAAGA ATGCAGTGAGTGGATCAGAATGTCTGCTTTCC VCAM1 2539 CAGGCACACACAGGTGGGACACAAAT 2540 TGGCTTCAGGAGCTGAATACCCTCCCAGGCACACACAGGTGG GACACAAATAAGGGTTTTGGAACCACTATTTTCTCATCACGACA GCA VCL 2543 AGTGGCAGCCACGGCGCC 2544 GATACCACAACTCCCATCAAGCTGTTGGCAGTGGCAGCCACG GCGCCTCCTGATGCGCCTAACAGGGA VCPIP1 2547 TGGTCCATCCTCTGCACCTGCTAC 2548 TTTCTCCCAGTACCATTCGTGATGGTCCATCCTCTGCACCTGC TACACCTACCAAGGCTCCCTATTCA VDR 2551 CAGCATGAAGCTAACGCCCCTTGT 2552 CCTCTCCTTCCAGCCTGAGTGCAGCATGAAGCTAACGCCCCTT GTGCTCGAAGTGTTTGGCAATGA VEGFA 2555 TTGCCTTGCTGCTCTACCTCCACCA 2556 CTGCTGTCTTGGGTGCATTGGAGCCTTGCCTTGCTGCTCTACC TCCACCATGCCAAGTGGTCCCAGGCTGC VEGFB 2559 CTGGGCAGCACCAAGTCCGGA 2560 TGACGATGGCCTGGAGTGTGTGCCCACTGGGCAGCACCAAGT CCGGATGCAGATCCTCATGATCCGGTACC VEGFC 2563 CCTCTCTCTCAAGGCCCCAAACCAGT 2564 CCTCAGCAAGACGTTATTTGAAATTACAGTGCCTCTCTCTCAAG GCCCCAAACCAGTAACAATCAGTTTTGCCAATCACACTT VIM 2567 ATTTCACGCATCTGGCGTTCCA 2568 TGCCCTTAAAGGAACCAATGAGTCCCTGGAACGCCAGATGCG TGAAATGGAAGAGAACTTTGCCGTTGAAGC VTI1B 2571 CGAAACCCCATGATGTCTAAGCTTCG 2572 ACGTTATGCACCCCTGTCTTTCCGAAACCCCATGATGTCTAAG CTTCGAAACTACCGGAAGGACCTTGCTAAACTCCATCGG WDR19 2575 CCCCTCGACGTATGTCTCCCATTC 2576 GAGTGGCCCAGATGTCCATAAGAATGGGAGACATACGTCGAG GGGTTAACCAAGCCCTCAAGCATC WFDC1 2579 CTATGAGTGCCACATCCTGAGCCC 2580 ACCCCTGCTCTGTCCCTCGGGCTATGAGTGCCACATCCTGAG CCCAGGTGACGTGGCCGAAGGTAT WISP1 2583 CGGGCTGCATCAGCACACGC 2584 AGAGGCATCCATGAACTTCACACTTGCGGGCTGCATCAGCACA CGCTCCTATCAACCCAAGTACTGTGGAGTTTG WNT5A 2587 TTGATGCCTGTCTTCGCGCCTTCT 2588 GTATCAGGACCACATGCAGTACATCGGAGAAGGCGCGAAGAC AGGCATCAAAGAATGCCAGTATCAATTCCGACA WWOX 2591 CTGCTGTTTACCTTGGCGAGGCCTTTC 2592 ATCGCAGCTGGTGGGTGTACACACTGCTGTTTACCTTGGCGAG GCCTTTCACCAAGTCCATGCAACAGGGAGCT XIAP 2595 TCCCCAAATTGCAGATTTATCAACGGC 2596 GCAGTTGGAAGACACAGGAAAGTATCCCCAAATTGCAGATTTA TCAACGGCTTTTATCTTGAAAATAGTGCCACGCA XRCC5 2599 TCTGGCTGAAGGCAGTGTCACCTC 2600 AGCCCACTTCAGCGTCTCCAGTCTGGCTGAAGGCAGTGTCAC CTCTGTTGGAAGTGTGAATCCTGCT YY1 2603 TTGATCTGCACCTGCTTCTGCTCC 2604 ACCCGGGCAACAAGAAGTGGGAGCAGAAGCAGGTGCAGATCA AGACCCTGGAGGGCGAGTTCTCGGTC ZFHX3 2607 ACCTGGCCCAACTCTACCAGCATC 2608 CTGTGGAGCCTCTGCCTGCGGACCTGGCCCAACTCTACCAGC ATCAGCTCAATCCAACCCTGCTCC ZFP36 2611 CAGGTCCCCAAGTGTGCAAGCTC 2612 CATTAACCCACTCCCCTGACCTCACGCTGGGGCAGGTCCCCA AGTGTGCAAGCTCAGTATTCATGATGGTGGGGG ZMYND8 2615 CTTTTGCAGGCCAGAATGGAAACC 2616 GGTCTGGGCCAAACTGAAGGGGTTTCCATTCTGGCCTGCAAAA GCTCTAAGGGATAAAGACGGGCA ZNF3 2619 AGGAGGTTCCACACTCGCCAGTTC 2620 CGAAGGGACTCTGCTCCAGTGAACTGGCGAGTGTGGAACCTC CTGACACCTTCTGAGGACCTCCTGC ZNF827 2623 CCCGCCTTCAGAGAAGAAACCAGA 2624 TGCCTGAGGACCCTCTACCGCCCCCGCCTTCAGAGAAGAAAC CAGAAAAAGTCACTCCGCCACCTC ZWINT 2627 ACCAAGGCCCTGACTCAGATGGAG 2628 TAGAGGCCATCAAAATTGGCCTCACCAAGGCCCTGACTCAGAT GGAGGAAGCCCAGAGGAAACGGA

TABLE B microRNA Sequence SEQ ID NO hsa-miR-1 UGGAAUGUAAAGAAGUAUGUAU 2629 hsa-miR-103 GCAGCAUUGUACAGGGCUAUGA 2630 hsa-miR-106b UAAAGUGCUGACAGUGCAGAU 2631 hsa-miR-10a UACCCUGUAGAUCCGAAUUUGUG 2632 hsa-miR-133a UUUGGUCCCCUUCAACCAGCUG 2633 hsa-miR-141 UAACACUGUCUGGUAAAGAUGG 2634 hsa-miR-145 GUCCAGUUUUCCCAGGAAUCCCU 2635 hsa-miR-146b-5p UGAGAACUGAAUUCCAUAGGCU 2636 hsa-miR-150 UCUCCCAACCCUUGUACCAGUG 2637 hsa-miR-152 UCAGUGCAUGACAGAACUUGG 2638 hsa-miR-155 UUAAUGCUAAUCGUGAUAGGGGU 2639 hsa-miR-182 UUUGGCAAUGGUAGAACUCACACU 2640 hsa-miR-191 CAACGGAAUCCCAAAAGCAGCUG 2641 hsa-miR-19b UGUAAACAUCCUCGACUGGAAG 2642 hsa-miR-200c UAAUACUGCCGGGUAAUGAUGGA 2643 hsa-miR-205 UCCUUCAUUCCACCGGAGUCUG 2644 hsa-miR-206 UGGAAUGUAAGGAAGUGUGUGG 2645 hsa-miR-21 UAGCUUAUCAGACUGAUGUUGA 2646 hsa-miR-210 CUGUGCGUGUGACAGCGGCUGA 2647 hsa-miR-22 AAGCUGCCAGUUGAAGAACUGU 2648 hsa-miR-222 AGCUACAUCUGGCUACUGGGU 2649 hsa-miR-26a UUCAAGUAAUCCAGGAUAGGCU 2650 hsa-miR-27a UUCACAGUGGCUAAGUUCCGC 2651 hsa-miR-27b UUCACAGUGGCUAAGUUCUGC 2652 hsa-miR-29b UAGCACCAUUUGAAAUCAGUGUU 2653 hsa-miR-30a CUUUCAGUCGGAUGUUUGCAGC 2654 hsa-miR-30e-5p CUUUCAGUCGGAUGUUUACAGC 2655 hsa-miR-31 AGGCAAGAUGCUGGCAUAGCU 2656 hsa-miR-331 GCCCCUGGGCCUAUCCUAGAA 2657 hsa-miR-425 AAUGACACGAUCACUCCCGUUGA 2658 hsa-miR-449a UGGCAGUGUAUUGUUAGCUGGU 2659 hsa-miR-486-5p UCCUGUACUGAGCUGCCCCGAG 2660 hsa-miR-92a UAUUGCACUUGUCCCGGCCUGU 2661 hsa-miR-93 CAAAGUGCUGUUCGUGCAGGUAG 2662 hsa-miR-99a AACCCGUAGAUCCGAUCUUGUG 2663 

1.-20. (canceled)
 21. A method of analyzing expression of RNA transcripts of genes in a patient with prostate cancer, comprising: measuring a level of an RNA transcript, in a sample from the patient comprising prostate tumor tissue, of a set of genes consisting of: (a) at least one gene selected from the group consisting of genes listed in Table 3A; and (b) at least one gene selected from the group consisting of genes listed in Table 3B; and (c) at least one reference gene.
 22. The method of claim 21, wherein the at least one gene selected from the group consisting of genes listed in Table 3A includes at least one of BGN, COL1A1, SFRP4, and TPX2.
 23. The method of claim 22, wherein the RNA transcript level of the at least one of BGN, COL1A1, SFRP4, and TPX2 is measured using at least one of the following sets of oligonucleotides: SEQ ID Nos: 257, 258, and 259 (for BGN); SEQ ID Nos: 501, 502, and 503 (for COL1A1); SEQ ID Nos: 2157, 2158, and 2159 (for SFRP4); and SEQ ID Nos: 2449, 2450, and 2451 (for TPX2).
 24. The method of claim 21, wherein the at least one gene selected from the group consisting of genes listed in Table 3B includes at least one of FLNC, GSN, GSTM2, TPM2, AZGP1, KLK2, FAM13C, and SRD5A2.
 25. The method of claim 24, wherein the RNA transcript level of the at least one of FLNC, GSN, GSTM2, TPM2, AZGP1, KLK2, FAM13C, and SRD5A2 is measured using at least one of the following sets of oligonucleotides: SEQ ID Nos: 929, 930, and 931 (for FLNC); SEQ ID Nos: 1029, 1030, and 1031 (for GSN); SEQ ID Nos: 1037, 1038, and 1039 (for GSTM2); SEQ ID Nos: 2441, 2442, and 2443 (for TPM2); SEQ ID Nos: 225, 226, and 227 (for AZGP1); SEQ ID Nos: 1361, 1362, and 1363 (for KLK2); SEQ ID Nos: 857, 858, and 859 (for FAM13C); and SEQ ID Nos: 2273, 2274, and 2275 (for SRD5A2).
 26. The method of claim 21, wherein the at least one gene selected from the group consisting of genes listed in Table 3A includes at least one of BGN, COL1A1, SFRP4, and TPX2; and wherein the at least one gene selected from the group consisting of genes listed in Table 3B includes at least one of FLNC, GSN, GSTM2, TPM2, AZGP1, KLK2, FAM13C, and SRD5A2.
 27. The method of claim 26, wherein the RNA transcript level of the at least one of BGN, COL1A1, SFRP4, and TPX2 is measured using at least one of the following sets of oligonucleotides: SEQ ID Nos: 257, 258, and 259 (for BGN); SEQ ID Nos: 501, 502, and 503 (for COL1A1); SEQ ID Nos: 2157, 2158, and 2159 (for SFRP4); and SEQ ID Nos: 2449, 2450, and 2451 (for TPX2); and wherein the RNA transcript level of the at least one of FLNC, GSN, GSTM2, TPM2, AZGP1, KLK2, FAM13C, and SRD5A2 is measured using at least one of the following sets of oligonucleotides: SEQ ID Nos: 929, 930, and 931 (for FLNC); SEQ ID Nos: 1029, 1030, and 1031 (for GSN); SEQ ID Nos: 1037, 1038, and 1039 (for GSTM2); SEQ ID Nos: 2441, 2442, and 2443 (for TPM2); SEQ ID Nos: 225, 226, and 227 (for AZGP1); SEQ ID Nos: 1361, 1362, and 1363 (for KLK2); SEQ ID Nos: 857, 858, and 859 (for FAM13C); and SEQ ID Nos: 2273, 2274, and 2275 (for SRD5A2).
 28. The method of claim 21, wherein the at least one gene selected from the group consisting of genes listed in Table 3A includes each of BGN, COL1A1, SFRP4, and TPX2.
 29. The method of claim 21, wherein the at least one gene selected from the group consisting of genes listed in Table 3B includes each of FLNC, GSN, GSTM2, TPM2, AZGP1, KLK2, FAM13C, and SRD5A2.
 30. The method of claim 21, wherein the at least one gene selected from the group consisting of genes listed in Table 3A includes each of BGN, COL1A1, SFRP4, and TPX2; and wherein the at least one gene selected from the group consisting of genes listed in Table 3B includes each of FLNC, GSN, GSTM2, TPM2, AZGP1, KLK2, FAM13C, and SRD5A2.
 31. The method of claim 21, wherein the at least one reference gene is a gene that does not exhibit a significantly different RNA expression level in cancerous prostate tissue compared to non-cancerous prostate tissue.
 32. The method of claim 21, wherein the at least one reference gene consists of from 1 to 6 reference genes.
 33. The method of claim 21, wherein the at least one reference gene comprises one or more of AAMP, ARF1, ATP5E, CLTC, EEF1A1, GPS1, GPX1, and PGK1.
 34. The method of claim 21, wherein the biological sample has a positive TMPRSS2 fusion status.
 35. The method of claim 21, wherein the biological sample has a negative TMPRSS2 fusion status.
 36. The method of claim 21, wherein the patient has early-stage prostate cancer.
 37. The method of claim 21, wherein the biological sample comprises prostate tumor tissue with the primary Gleason pattern for said prostate tumor.
 38. The method of claim 21, wherein the biological samples comprises prostate tumor tissue with the highest Gleason pattern for said prostate tumor.
 39. The method of claim 21, wherein the tissue sample comprises non-tumor prostate tissue.
 40. The method of claim 21, wherein the patient is receiving active surveillance treatment. 